Evaluation of cas9 molecule/guide rna molecule complexes

ABSTRACT

Disclosed herein are methods for evaluation, selection, optimization, and design of Cas9 molecule/gRNA molecule complexes.

RELATED APPLICATIONS

The present application is a continuation of U.S. application Ser. No.15/569,053, filed Oct. 24, 2017, which is a U.S. National Phase ofInternational Application No. PCT/US2016/029252, filed Apr. 25, 2016,which claims priority to U.S. Provisional Application No. 62/152,473,filed Apr. 24, 2015, all of which are incorporated by reference hereinin their entirety, including drawings.

FIELD OF THE INVENTION

The present invention(s) relates to the evaluation, selection, anddesign of Cas9 molecule/guide RNA (gRNA) molecule complexes.

SEQUENCE LISTING

This application contains a Sequence Listing, which was submitted inASCII format via EFS-Web, and is hereby incorporated by reference in itsentirety. The ASCII copy, created on Nov. 16, 2021, is namedSequenceListing.txt and is 193 KB in size.

BACKGROUND

Direct delivery of Cas9 ribonucleoprotein (RNP) complexes allows forefficient gene-editing while minimizing off-target activity owing to therapid turnover of the Cas9 proteins in cells. Gene editing can beachieved in various mammalian cells by cationic lipid delivery ofpurified Cas9 proteins complexed with in vitro transcribed or chemicallysynthesized guide RNA (gRNA). Efficiency of gene editing mediated by RNPdelivery varies by locus and depends on the length of gRNA, as well asthe amount and ratio of the Cas9 protein and the gRNA delivered. Giventhe two-component nature of the RNP complex, precise conditions arerequired to obtain a complete and productive complex formation betweenCas9 protein and gRNA. While the amount of protein and RNA can bequantitated by dye-binding assays, e.g., the Bradford dye binding assayor the riboquant RNA assay, these techniques do not provide aquantitation of the productive RNP complex necessary for gene editingactivity.

Structural and biophysical characterization of Cas9/gRNA complexesrevealed a large contact area and a high affinity. Thermal melt curvesare a useful property to characterize the stability and binding ofprotein-ligand complexes. Differential Scanning Fluorimetry (DSF) is abiophysical technique where the change in fluorescence of a smallmolecule dye, e.g., SYPRO® orange, is used to monitor the thermaldenaturation of a protein and to determine its thermal meltingtemperature ( ). Binding of ligands to the protein tend to stabilize theprotein to differing extents and change its T_(m). Measurement of theT_(m) of a protein at different ligand concentrations can allow themeasurement of the affinity of protein for that ligand. A wide range ofthe thermal melting signature can be used to rapidly assay the qualityof RNP complexes at a high throughput with a high signal to noise ratio.

Thus, there remains a need for developing assays, such as DSF, that canbe used to evaluate the quality of Cas9 molecule/gRNA moleculecomplexes, e.g., to quantitate productive complex formation, aprerequisite for RNP mediated gene editing.

SUMMARY OF THE INVENTION

Methods are provided herein for screening for a Cas9 molecule/gRNAmolecule complex for administration to a subject that includes (a)generating a plurality of samples, each sample comprising a Cas9molecule/gRNA molecule complex generated by combining a Cas9 moleculeand one of a plurality of gRNA molecules; (b) detecting a meltingtemperature (T_(m)) value of the Cas9 molecule/gRNA molecule complex ineach of the plurality of samples; and (c) selecting at least one samplefrom the plurality of samples based on one or more of (i) a comparisonof the T_(m) values in the plurality of samples to a T_(m) value of areference Cas9 molecule/gRNA molecule complex or a pre-determinedthreshold T_(m) value, or (ii) a relative ordering of the T_(m) valuesof the plurality of samples. In certain embodiments, the step ofdetecting the T_(m) value of the Cas9 molecule/gRNA molecule complex ineach sample of the plurality of samples may include assessing eachsample in the plurality of samples by differential scanning fluorimetry(DSF). In certain embodiments, the gRNA may be a chimeric gRNA. Incertain embodiments, the gRNA may be a modular gRNA. In certainembodiments, the sample may comprise a component comprising an additive,a small molecule, a stabilizing reagent, buffer, pH, salt concentration,glycerol concentration, or other buffer component. In certainembodiments, a sample comprising a Cas9 molecule/gRNA molecule complexhaving a T_(m) of at least 8° C. greater than a T_(m) value of the Cas9molecule absent the gRNA molecule may be selected.

Provided herein in certain embodiments are isolated complexes of a Cas9molecule and a gRNA molecule having a T_(m) at least 8° C. greater thana T_(m) value of the Cas9 molecule absent the gRNA molecule selectedaccording to the methods provided herein.

Provided herein in certain embodiments are compositions including anisolated complex of a Cas9 molecule and a gRNA molecule having a T_(m)at least 8° C. greater than a T_(m) of the Cas9 molecule absent the gRNAmolecule selected according to the methods provided herein. In certainembodiments, the difference of the T_(m) of the non-naturally occurringcomplex of a Cas9 molecule and a gRNA molecule and the T_(m) of the Cas9molecule absent the gRNA molecule may be assessed by DSF. In certainembodiments, the gRNA may be a chimeric or modular gRNA.

Provided herein in certain embodiments are methods of determining thestability of a Cas9 molecule/gRNA molecule complex including (a)generating a plurality of Cas9 molecule/gRNA molecule complexes, eachcomprising a Cas9 molecule/gRNA molecule complex generated by combininga Cas9 molecule and one of a plurality of gRNA molecules; (b) detectinga T_(m) value of each of the Cas9 molecule/gRNA molecule complexes ofthe plurality of Cas9 molecule/gRNA molecule complexes; and (c)determining one or more of the plurality of Cas9 molecule/gRNA moleculecomplexes is stable if the T_(m) value of the Cas9 molecule/gRNAmolecule complex is greater than a T_(m) value of a reference moleculeor a T_(m) reference value.

In certain embodiments of the methods herein, the plurality of gRNAmolecules may be a library of candidate gRNA molecules. In certainembodiments, the library of candidate gRNA molecules may comprise alibrary of tracrRNA molecules or sequences. In certain embodiments, thelibrary of tracrRNA molecules or sequences may be of differing length.

Provided herein in certain embodiments are methods of determining acondition that promotes a stable Cas9 molecule/gRNA molecule complexincluding (a) combining a Cas9 molecule and a gRNA molecule in a sampleto form a Cas9 molecule/gRNA molecule complex; (b) detecting a T_(m)value of the Cas9 molecule/gRNA molecule complex; and (c) determiningthe Cas9 molecule/gRNA molecule complex is stable if the T_(m) value ofthe Cas9 molecule/gRNA molecule complex is greater than a T_(m) value ofa reference molecule or a T_(m) reference value.

Provided herein in certain embodiments are methods of screening for astable Cas9 molecule/gRNA molecule complex including (a) detecting aT_(m) value of a Cas9 molecule/gRNA molecule complex via DSF; and (b)determining the Cas9 molecule/gRNA molecule complex is stable if theT_(m) value of the Cas9 molecule/gRNA molecule complex is greater than aT_(m) value of a reference molecule or a T_(m) reference value.

Provided herein in certain embodiments are methods for identifying anoptimal gRNA to form a stable Cas9 molecule/gRNA molecule complexincluding (a) combining a Cas9 molecule and a gRNA molecule in a sampleto form the Cas9 molecule/gRNA molecule complex; (b) detecting a T_(m)value of the Cas9 molecule/gRNA molecule complex; and (c) determiningthe Cas9 molecule/gRNA molecule complex is stable if the T_(m) value ofthe Cas9 molecule/gRNA molecule complex is greater than a T_(m) value ofa reference molecule or a T_(m) reference value by at least 8° C.

Provided herein in certain embodiments are methods of determining thestability of a Cas9 molecule/gRNA molecule complex including (a)combining a Cas9 molecule and a gRNA molecule in a sample to form theCas9 molecule/gRNA molecule complex; (b) detecting a T_(m) value of theCas9 molecule/gRNA molecule complex; (c) measuring an activity value ofthe Cas9 molecule/gRNA molecule complex; and (d) determining the Cas9molecule/gRNA molecule complex is stable if (i) the T_(m) value of theCas9 molecule/gRNA molecule complex is greater than a T_(m) value of areference molecule or a T_(m) reference value and (ii) the activityvalue of the Cas9 molecule/gRNA molecule complex is greater than anactivity value of a reference molecule or an activity reference value.

Provided herein in certain embodiments are methods of optimizing bindingof a gRNA molecule to a Cas9 molecule to form a stable Cas9molecule/gRNA molecule complex including (a) combining the Cas9 moleculeand the gRNA molecule in a sample to form a Cas9 molecule/gRNA moleculecomplex; (b) detecting a T_(m) value of the Cas9 molecule/gRNA moleculecomplex; (c) determining a delta value between the T_(m) value of theCas9 molecule/gRNA molecule complex and a T_(m) value of a referencemolecule or a T_(m) reference value; and (d) determining the Cas9molecule/gRNA molecule complex is stable if the delta value is at least8° C. and the T_(m) value of the Cas9 molecule/gRNA molecule complex isgreater than the T_(m) value of the reference molecule or the T_(m)reference value.

Provided herein in certain embodiments are methods of detecting a stableCas9 molecule/gRNA molecule complex including (a) detecting athermostability value of a reference molecule; (b) combining a Cas9molecule and a gRNA molecule in a sample to form a Cas9 molecule/gRNAmolecule complex; (c) measuring a thermostability value of the Cas9molecule/gRNA molecule complex; and (d) determining the Cas9molecule/gRNA molecule complex is stable if the thermostability value ofthe Cas9 molecule/gRNA molecule complex is greater than thethermostability value of the reference molecule.

In certain embodiments of the methods herein, the thermostability valuemay be a denaturation temperature value and the thermostabilityreference value may be a denaturation temperature reference value. Incertain embodiments of the methods herein, the thermostability value maybe a T_(m) value and the thermostability reference value may be a T_(m)reference value.

In certain embodiments of the methods herein, the Cas9 molecule/gRNAmolecule complex may be stable if the T_(m) value of the Cas9molecule/gRNA molecule complex is at least 1° C., at least 2° C., atleast 3° C., at least 4° C., at least 5° C., at least 6° C., at least 7°C., at least 8° C., at least 9° C., at least 10° C., at least 11° C., atleast 12° C., at least 13° C., at least 14° C., at least 15° C., atleast 16° C., at least 17° C., at least 18° C., at least 19° C., or atleast 20° C. greater than the T_(m) value of the reference molecule orT_(m) reference value. For example, in certain embodiments, the Cas9molecule/gRNA molecule complex is stable if the T_(m) value of the Cas9molecule/gRNA molecule complex is at least 8° C. greater than the T_(m)value of the reference molecule or T_(m) reference value.

In certain embodiments of the methods herein, the Cas9 molecule/gRNAmolecule complex may be stable if the T_(m) value of the Cas9molecule/gRNA molecule complex is about 1° C., about 2° C., about 3° C.,about 4° C., about 5° C., about 6° C., about 7° C., about 8° C., about9° C., about 10° C., about 11° C., about 12° C., about 13° C., about 14°C., about 15° C., about 16° C., about 17° C., about 18° C., about 19°C., or about 20° C. greater than the T_(m) value of the referencemolecule or T_(m) reference value. For example, in certain embodiments,the Cas9 molecule/gRNA molecule complex is stable if the T_(m) value ofthe Cas9 molecule/gRNA molecule complex is about 8° C. greater than theT_(m) value of the reference molecule or T_(m) reference value.

In certain embodiments of the methods herein, the Cas9 molecule/gRNAmolecule complex may be stable if the T_(m) value of the Cas9molecule/gRNA molecule complex is about ° C. to 5° C., about 6° C. to10° C., about 11° C. to 15° C., or about 16° C. to 20° C. greater thanthe T_(m) value of the reference molecule or T_(m) reference value. Forexample, in certain embodiments, the Cas9 molecule/gRNA molecule complexis stable if the T_(m) value of the Cas9 molecule/gRNA molecule complexis about 6° C. to 10° C. greater than the T_(m) value of the referencemolecule or T_(m) reference value.

In certain embodiments of the methods herein, the T_(m) value may bedetected using a thermal shift assay. In certain embodiments, thethermal shift assay may be selected from DSF, differential scanningcalorimetry (DSC), or isothermal titration calorimetry (ITC).

In certain embodiments of the methods herein, the gRNA molecule maycomprise a chimeric gRNA molecule. In certain embodiments, the gRNAmolecule may comprise a modular gRNA molecule.

In certain embodiments of the methods herein, the Cas9 molecule may beany of the Cas9 molecules disclosed herein. For example, the Cas9molecule may be a Cas9 molecule selected from Table 1. In certainembodiments, the Cas9 molecule may be a chimeric Cas9 molecule, or asynthetic or engineered Cas9 molecule. For example, the Cas9 moleculemay be a Cas9 molecule with a portion or portions deleted. In certainembodiments, the Cas9 molecule may comprise a S. pyogenes or a S. aureusCas9 molecule.

In certain embodiments of the methods herein, the reference molecule maybe selected from (a) a reference Cas9 molecule in the absence of a gRNAmolecule; (b) a reference Cas9 molecule (e.g., the same Cas9 molecule asthe Cas9 molecule in the complex being evaluated) complexed with asecond gRNA molecule (i.e., a gRNA other than the one in the complexbeing evaluated); and (c) a reference Cas9 molecule/gRNA moleculecomplex, wherein the reference Cas9 molecule/gRNA molecule was formedunder different conditions, e.g., with different proportions of Cas9molecule and gRNA molecule, than the Cas9 molecule/gRNA moleculecomplex, or was formed in a different buffer. In certain embodiments,the reference Cas9 molecule may be the same as the Cas9 molecule of thecomplex being evaluated. In certain embodiments, the reference Cas9molecule may be different from the Cas9 molecule of the complex beingevaluated. In certain embodiments, the reference Cas9 molecule maydiffer in primary sequence from the Cas9 molecule of the complex beingevaluated. In certain embodiments, the gRNA molecule of the referenceCas9 molecule/gRNA molecule complex may be the same as the gRNA moleculeof the complex being evaluated. In certain embodiments, the gRNAmolecule of the reference Cas9 molecule/gRNA molecule complex may bedifferent from the gRNA molecule of the complex being evaluated. Incertain embodiments, the gRNA molecule of the reference Cas9molecule/gRNA molecule complex may differ in sequence or differs by amodification from the gRNA molecule of the complex being evaluated.

In certain embodiments of the methods herein, the T_(m) reference valuemay comprise a preselected numerical value for T_(m). In certainembodiments, the T_(m) reference value may comprise a value correlatedwith the T_(m) of any of the reference molecules described herein.

In certain embodiments, the methods disclosed herein may further includedetecting an activity of the Cas9 molecule/gRNA molecule complex;measuring an activity value of the Cas9 molecule/gRNA molecule complex;and determining the Cas9 molecule/gRNA molecule complex is stable if theactivity value of the Cas9 molecule/gRNA molecule complex is greaterthan the activity value of a reference molecule or an activity referencevalue. In certain embodiments, the activity may comprise one or more of:an ability to induce indels; an ability to modify a target DNA; apropensity of a preselected repair method; an ability of the gRNAmolecule to remain hybridized to the DNA target; and an ability of thegRNA molecule to bind to the Cas9 molecule of the Cas9 molecule/gRNAmolecule complex. In certain embodiments, the activity value may be abinding value and the activity may be the ability of the gRNA moleculeto bind to the Cas9 molecule comprising: (a) combining the gRNA moleculeand the Cas9 molecule in a sample to form the Cas9 molecule/gRNAmolecule complex; (b) measuring a binding value of the Cas9molecule/gRNA molecule complex; and (c) determining the Cas9molecule/gRNA molecule complex is stable if the binding value of theCas9 molecule/gRNA molecule complex is greater than the binding value ofa reference molecule or the binding reference value. In certainembodiments, the binding value may be measured using a kinetics assay.In certain embodiments, the kinetics assay may be selected from surfaceplasmon resonance (SPR) assay, Bio-Layer Interferometry (BLI) assay, orgel band shift assay. In certain embodiments, the propensity of apreselected repair method may be HDR or NHEJ. In certain embodiments,the activity of the Cas9 molecule/gRNA molecule complex may be testedusing an in vitro system; an ex vivo system; an in vivo system; acellular assay; or an animal model.

In certain embodiments, the reference molecule is selected from any ofthe reference molecules provided herein. In certain embodiments, thereference Cas9 molecule/gRNA molecule complex is formed with differentproportions of Cas9 molecule and gRNA molecule than the Cas9molecule/gRNA molecule complex or is formed in a different buffer thanthe Cas9 molecule/gRNA molecule complex.

Provided herein in certain embodiments are synthetic Cas9 molecule/gRNAmolecule complexes generated using any of the methods described herein.

Provided herein in certain embodiments are compositions comprising Cas9molecule/gRNA molecule complexes generated using any of the methodsdescribed herein.

Provided herein in certain embodiments are vector systems comprising anucleic acid encoding one or more Cas9 molecule/gRNA molecule complexesgenerated using the any of the methods described herein.

Provided herein in certain embodiments are methods of delivering a Cas9molecule/gRNA molecule complex to a target cell comprising deliveringany of the Cas9 molecule/gRNA molecule complexes described herein to thetarget cell. In certain embodiments, the Cas9 molecule/gRNA moleculecomplexes may be delivered to the cell by RNP cationic lipidtransfection, a viral vector, or RNA transfection. In certainembodiments, the viral vector may be an AAV vector.

In certain embodiments, the gRNA molecule in a method, composition, orformulation provided herein may be a unimolecular or chimeric gRNA. Inother embodiments, the gRNA molecule may be a modular gRNA.

In certain embodiments, the Cas9 molecule in a method, composition, orformulation provided herein may be an S. pyogenes, S. aureus, or S.thermophilus Cas9 molecule, or a Cas9 molecule derived from an S.pyogenes, S. aureus, or S. thermophilus Cas9 molecule. In certainembodiments, the Cas9 molecule may be labeled, and in certain of theseembodiments the label may be a fluorescent dye.

Other features and advantages of the invention will be apparent from thedetailed description, drawings, and from the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1I are representations of several exemplary gRNAs.

FIG. 1A depicts a modular gRNA molecule derived in part (or modeled on asequence in part) from Streptococcus pyogenes (S. pyogenes) as aduplexed structure (SEQ ID NOs:39 and 40, respectively, in order ofappearance);

FIG. 1B depicts a unimolecular gRNA molecule derived in part from S.pyogenes as a duplexed structure (SEQ ID NO:41);

FIG. 1C depicts a unimolecular gRNA molecule derived in part from S.pyogenes as a duplexed structure (SEQ ID NO:42);

FIG. 1D depicts a unimolecular gRNA molecule derived in part from S.pyogenes as a duplexed structure (SEQ ID NO:43);

FIG. 1E depicts a unimolecular gRNA molecule derived in part from S.pyogenes as a duplexed structure (SEQ ID NO:44);

FIG. 1F depicts a modular gRNA molecule derived in part fromStreptococcus thermophilus (S. thermophilus) as a duplexed structure(SEQ ID NOs:45 and 46, respectively, in order of appearance);

FIG. 1G depicts an alignment of modular gRNA molecules of S. pyogenesand S. thermophilus (SEQ ID NOs:39, 45, 47, and 46, respectively, inorder of appearance).

FIGS. 1H-1I depicts additional exemplary structures of unimolecular gRNAmolecules.

FIG. 1H shows an exemplary structure of a unimolecular gRNA moleculederived in part from S. pyogenes as a duplexed structure (SEQ ID NO:42).

FIG. 1I shows an exemplary structure of a unimolecular gRNA moleculederived in part from S. aureus as a duplexed structure (SEQ ID NO:38).

FIGS. 2A-2G depict an alignment of Cas9 sequences (Chylinski 2013). TheN-terminal RuvC-like domain is boxed and indicated with a “Y.” The othertwo RuvC-like domains are boxed and indicated with a “B.” The HNH-likedomain is boxed and indicated by a “G.” Sm: S. mutans (SEQ ID NO:1); Sp:S. pyogenes (SEQ ID NO:2); St: S. thermophilus (SEQ ID NO:4); and Li: L.innocua (SEQ ID NO:5). “Motif” (SEQ ID NO: 14) is a consensus sequencebased on the four sequences. Residues conserved in all four sequencesare indicated by single letter amino acid abbreviation; “*” indicatesany amino acid found in the corresponding position of any of the foursequences; and “-” indicates absent.

FIGS. 3A-3B show an alignment of the N-terminal RuvC-like domain fromthe Cas9 molecules disclosed in Chylinski 2013 (SEQ ID NOs:52-95,120-123). The last line of FIG. 3B identifies 4 highly conservedresidues.

FIGS. 4A-4B show an alignment of the N-terminal RuvC-like domain fromthe Cas9 molecules disclosed in Chylinski 2013 with sequence outliersremoved (SEQ ID NOs:52-123). The last line of FIG. 4B identifies 3highly conserved residues.

FIGS. 5A-5C show an alignment of the HNH-like domain from the Cas9molecules disclosed in Chylinski 2013 (SEQ ID NOs:124-198). The lastline of FIG. 5C identifies conserved residues.

FIGS. 6A-6B show an alignment of the HNH-like domain from the Cas9molecules disclosed in Chylinski 2013 with sequence outliers removed(SEQ ID NOs:124-141, 148, 149, 151-153, 162, 163, 166-174, 177-187,194-198). The last line of FIG. 6B identifies 3 highly conservedresidues.

FIG. 7 illustrates gRNA domain nomenclature using an exemplary gRNAsequence (SEQ ID NO:42).

FIGS. 8A and 8B provide schematic representations of the domainorganization of S. pyogenes Cas9. FIG. 8A shows the organization of theCas9 domains, including amino acid positions, in reference to the twolobes of Cas9 (recognition (REC) and nuclease (NUC) lobes). FIG. 8Bshows the percent homology of each domain across 83 Cas9 orthologs.

FIG. 9A depicts the thermal stability of S. aureus Cas9 in the absenceof gRNA as determined by DSF.

FIG. 9B depicts the thermal stability of S. pyogenes Cas9 in the absenceof gRNA as determined by DSF.

FIG. 10 depicts the thermal stability of (1) S. pyogenes Cas9, (2) S.pyogenes Cas9 in the presence of S. pyogenes gRNA, and (3) S. pyogenesCas9 in the presence of S. aureus gRNA, as determined by DSF.

FIG. 11A depicts the thermal stability of (1) S. aureus Cas9 and (2)S.aureus Cas9 with gRNA targeting CD3, as determined by DSF.

FIG. 11B depicts exemplary FACS analysis showing the generation CD3negative population after delivery of S. aureus Cas9 and gRNA targetingCD3 to Jurkat T cells.

DETAILED DESCRIPTION Definitions

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Although methods and materialssimilar or equivalent to those described herein can be used in thepractice or testing of the present invention, suitable methods andmaterials are described below. All publications, patent applications,patents, and other references mentioned herein are incorporated byreference in their entirety. In addition, the materials, methods, andexamples are illustrative only and not intended to be limiting.

“Alt-HDR,” “alternative homology-directed repair,” or “alternative HDR”as used herein refers to the process of repairing DNA damage using ahomologous nucleic acid (e.g., an endogenous homologous sequence, e.g.,a sister chromatid, or an exogenous nucleic acid, e.g., a templatenucleic acid). Alt-HDR is distinct from canonical HDR in that theprocess utilizes different pathways from canonical HDR, and can beinhibited by the canonical HDR mediators, RAD51 and BRCA2. Also, alt-HDRuses a single-stranded or nicked homologous nucleic acid for repair ofthe break.

“Canonical HDR” or canonical homology-directed repair as used hereinrefers to the process of repairing DNA damage using a homologous nucleicacid (e.g., an endogenous homologous sequence, e.g., a sister chromatid,or an exogenous nucleic acid, e.g., a template nucleic acid). CanonicalHDR typically acts when there has been significant resection at thedouble strand break, forming at least one single stranded portion ofDNA. In a normal cell, HDR typically involves a series of steps such asrecognition of the break, stabilization of the break, resection,stabilization of single stranded DNA, formation of a DNA crossoverintermediate, resolution of the crossover intermediate, and ligation.The process requires RAD51 and BRCA2, and the homologous nucleic acid istypically double-stranded.

Unless indicated otherwise, the term “HDR” as used herein encompassesboth canonical HDR and alt-HDR.

“Non-homologous end joining” or “NHEJ” as used herein refers to ligationmediated repair and/or non-template mediated repair including canonicalNHEJ (cNHEJ), alternative NHEJ (altNHEJ), microhomology-mediated endjoining (MMEJ), single-strand annealing (SSA), and synthesis-dependentmicrohomology-mediated end joining (SD-MMEJ).

“Acquire” or “acquiring” as the terms are used herein, refer toobtaining possession of a physical entity, or a value, e.g., a numericalvalue, by one or more or all of: “directly acquiring,” “indirectlyacquiring” the physical entity or value, or in the case of a value,“acquiring by calculation.”

“Directly acquiring” means performing a process (e.g., performing asynthetic or analytical method) to obtain the physical entity or value.“Directly acquiring a physical entity includes performing a process thatincludes a physical change in a physical substance, e.g., a startingmaterial. Exemplary changes include making a physical entity from two ormore starting materials, shearing or fragmenting a substance, separatingor purifying a substance, combining two or more separate entities into amixture, performing a chemical reaction that includes breaking orforming a covalent or noncovalent bond. Directly acquiring a valueincludes performing a process that includes a physical change in asample or another substance, e.g., performing an analytical processwhich includes a physical change in a substance, e.g., a sample,analyte, or reagent (sometimes referred to herein as “physicalanalysis”), performing an analytical method, e.g., a method whichincludes one or more of the following: separating or purifying asubstance, e.g., an analyte, or a fragment or other derivative thereof,from another substance; combining an analyte, or fragment or otherderivative thereof, with another substance, e.g., a buffer, solvent, orreactant; or changing the structure of an analyte, or a fragment orother derivative thereof, e.g., by breaking or forming a covalent ornoncovalent bond, between a first and a second atom of the analyte; orby changing the structure of a reagent, or a fragment or otherderivative thereof, e.g., by breaking or forming a covalent ornoncovalent bond, between a first and a second atom of the reagent.

“Indirectly acquiring” refers to receiving the physical entity or valuefrom another party or source (e.g., a third party laboratory thatdirectly acquired the physical entity or value). E.g., a first party mayacquire a value from a second party (indirectly acquiring) which saidsecond party directly acquired or acquired by calculation.

“Acquiring by calculation” refers to acquiring a value by calculation orcomputation, e.g., as performed on a machine, e.g., a computer.

“Domain” as used herein is used to describe segments of a protein ornucleic acid. Unless otherwise indicated, a domain is not required tohave any specific functional property.

Calculations of homology or sequence identity between two sequences (theterms are used interchangeably herein) are performed as follows. Thesequences are aligned for optimal comparison purposes (e.g., gaps can beintroduced in one or both of a first and a second amino acid or nucleicacid sequence for optimal alignment and non-homologous sequences can bedisregarded for comparison purposes). The optimal alignment isdetermined as the best score using the GAP program in the GCG softwarepackage with a Blossum 62 scoring matrix with a gap penalty of 12, a gapextend penalty of 4, and a frame shift gap penalty of 5. The amino acidresidues or nucleotides at corresponding amino acid positions ornucleotide positions are then compared. When a position in the firstsequence is occupied by the same amino acid residue or nucleotide as thecorresponding position in the second sequence, then the molecules areidentical at that position. The percent identity between the twosequences is a function of the number of identical positions shared bythe sequences.

“Polypeptide” as used herein refers to a polymer of amino acids havingless than 100 amino acid residues. In certain embodiments, it has lessthan 50, 20, or 10 amino acid residues.

A “reference molecule” as used herein refers to a molecule to which amodified or candidate molecule is compared. For example, a referenceCas9 molecule refers to a Cas9 molecule to which a modified or candidateCas9 molecule is compared. Likewise, a reference gRNA refers to a gRNAmolecule to which a modified or candidate gRNA molecule is compared.Additionally, a reference Cas9 molecule/gRNA molecule complex refers toa Cas9 molecule/gRNA molecule complex to which a Cas9 molecule/gRNAmolecule complex is compared. The modified or candidate molecule may becompared to the reference molecule on the basis of sequence (e.g., themodified or candidate molecule may have X % sequence identity orhomology with the reference molecule), thermostability, or activity(e.g., the modified or candidate molecule may have X % of the activityof the reference molecule). For example, where the reference molecule isa Cas9 molecule, a modified or candidate molecule may be characterizedas having no more than 10% of the nuclease activity of the referenceCas9 molecule. Examples of reference Cas9 molecules include naturallyoccurring unmodified Cas9 molecules, e.g., a naturally occurring Cas9molecule from S. pyogenes, S. aureus, S. thermophilus, or N.meningitidis. In certain embodiments, the reference Cas9 molecule is thenaturally occurring Cas9 molecule having the closest sequence identityor homology with the modified or candidate Cas9 molecule to which itisbeing compared. In certain embodiments, the reference Cas9 molecule is aparental molecule having a naturally occurring or known sequence onwhich a mutation has been made to arrive at the modified or candidateCas9 molecule.

“Reference value” as used herein refers to a reference value that is apreselected numerical value. The preselected numerical value can be asingle number or a range. In certain embodiments, the reference valuemay comprise a value correlated with a value of a reference molecule. Incertain embodiments, the reference value may be a thermostabilityreference value. In certain embodiments, the thermostability referencevalue is a preselected numerical value for thermostability. In certainembodiments, a thermostability reference value may comprise a valuecorrelated with a thermostability value of a reference molecule. Incertain embodiments, a thermostability reference value may comprise aparameter correlated with thermostability. In certain embodiments, thethermostability reference value may be a denaturation temperaturereference value or a melting temperature (T_(m)) reference value. Incertain embodiments, the denaturation temperature reference value is apreselected numerical value for denaturation. In certain embodiments,the denaturation temperature reference value may comprise a valuecorrelated with a denaturation temperature value of a referencemolecule. In certain embodiments, the denaturation temperature referencevalue may comprise a parameter correlated with denaturation. In certainembodiments, the T_(m) reference value may be a preselected numericalvalue for T_(m). In certain embodiments, the T_(m) reference value maybe a pre-determined threshold T_(m). In certain embodiments, the T_(m)reference value may comprise a value correlated with a T_(m) value of areference molecule. In certain embodiments, the T_(m) reference valuemay comprise a parameter correlated with T_(m). In certain embodiments,the reference value may be an activity reference value. In certainembodiments, the activity reference value may comprise a valuecorrelated with activity value of a reference molecule. In certainembodiments, the activity reference value may comprise a parametercorrelated with an activity. In certain embodiments, the activityreference value may be a cleavage reference value or a binding referencevalue. In certain embodiments, the cleavage reference value may be apreselected numerical value for cleavage of a nucleic acid. In certainembodiments, the binding reference value may be a preselected numericalvalue for binding of two or more molecules. In certain embodiments thereference value may be a delta reference value. In certain embodiments,the delta reference value may be a preselected numerical value for adelta value.

“Delta value” as used herein is a value representing the difference orshift between two values. For example, in certain embodiments, a deltavalue may be a value representing the difference between athermostability value of a Cas9 molecule/gRNA molecule complex beingevaluated and a thermostability value of a reference molecule or athermostability reference value. In certain embodiments, a delta valuemay be a value representing the difference between the activity value ofthe Cas9 molecule/gRNA molecule complex being evaluated and the activityvalue of a reference molecule or an activity reference value.

“Replacement” or “replaced” as used herein with reference to amodification of a molecule does not require a process limitation butmerely indicates that the replacement entity is present.

“Subject” as used herein may mean either a human or non-human animal.The term includes, but is not limited to, mammals (e.g., humans, otherprimates, pigs, rodents (e.g., mice and rats or hamsters), rabbits,guinea pigs, cows, horses, cats, dogs, sheep, and goats). In certainembodiments, the subject is a human. In another embodiment, the subjectis poultry. In certain embodiments, the subject is a human, and incertain of these embodiments the human is an infant, child, young adult,or adult.

“X” as used herein in the context of an amino acid sequence refers toany amino acid (e.g., any of the twenty natural amino acids) unlessotherwise specified.

“About” as used herein means within 10% of a stated value or a range ofvalues.

A “Cas9 molecule” or “Cas9 polypeptide” as used herein refers to amolecule or polypeptide, respectively, that can interact with a gRNAmolecule and, in concert with the gRNA molecule, localize to a sitecomprising a target domain and, in certain embodiments, a PAM sequence.Cas9 molecules and Cas9 polypeptides include both naturally occurringCas9 molecules and Cas9 polypeptides and engineered, altered, ormodified Cas9 molecules or Cas9 polypeptides that differ, e.g., by atleast one amino acid residue, from a reference sequence, e.g., the mostsimilar naturally occurring Cas9 molecule.

Overview

The inventors have discovered that the stability of a Cas9 molecule/gRNAmolecule complex as determined by DSF is correlated with a variety ofproperties of the Cas9 molecule/gRNA molecule complex. As such, adetermination of stability can be used to evaluate a Cas9 molecule/gRNAmolecule complex (or a component thereof) for a variety of properties,e.g., the ability to cleave a target, the propensity of a cleavage eventmediated by a Cas9 molecule/gRNA molecule complex to be resolved by aparticular pathway, e.g., HDR or NHEJ, the ability to modulate a target,or suitability for a preselected delivery method. The determination ofstability can also be used to evaluate a Cas9 molecule, a gRNA molecule,a method of preparing a complex (e.g., the proportion or stoichiometryof the components), or the addition of an additional component, e.g., onthe efficacy or robustness of a Cas9 molecule/gRNA molecule complex, andgenerally for inclusion in a Cas9 molecule/gRNA molecule complex.

Provided herein based on the disclosed experimental results are methodsthat include measuring the thermostability of a Cas9/molecule gRNAmolecule complex. The thermostability of a protein can increase underfavorable conditions such as the addition of a binding RNA molecule,e.g., a gRNA. Thus, information regarding the thermostability of aCas9/gRNA complex is useful for determining whether the complex isstable. The methods that may include a step of measuring thethermostability of a Cas9/molecule gRNA molecule complex include,without limitation, methods of determining the stability of a Cas9molecule/gRNA molecule complex, methods of determining a condition thatpromotes a stable Cas9 molecule/gRNA molecule complex, methods ofscreening for a stable Cas9 molecule/gRNA molecule complex, methods foridentifying an optimal gRNA to form a stable Cas9 molecule/gRNA moleculecomplex, methods of screening for a Cas9/gRNA complex for administrationto a subject, and methods of selecting a Cas9/gRNA complex foradministration to a subject. In certain embodiments, the thermostabilityvalue of a Cas9 molecule/gRNA molecule complex may be measured.Additionally, in certain embodiments, the thermostability value of areference molecule may also be measured. In certain embodiments, theCas9 molecule/gRNA molecule complex may be determined to be stable ifthe thermostability value of the Cas9 molecule/gRNA molecule complex isgreater than the thermostability value of the reference molecule or athermostability reference value as described herein. In certainembodiments, the reference molecule may be the Cas9 molecule absent thegRNA molecule. In certain embodiments, the thermostability value that ismeasured may be a denaturation temperature value. In these embodiments,the thermostability reference value is a denaturation temperaturereference value. In certain embodiments, the thermostability value thatis measured may be a T_(m) value. In these embodiments, thethermostability reference value may be a T_(m) reference value. Incertain embodiments, the thermostability value may be measured using athermal shift assay. As disclosed herein, DSF is a technique that may beused to measure the thermostability of a protein. In certainembodiments, the thermal shift assay used to measure the thermostabilitymay be DSF, differential scanning calorimetry (DSC) or isothermaltitration calorimetry (ITC). In certain embodiments, the Cas9molecule/gRNA molecule complex may be determined to be stable if thethermostability value of the Cas9 molecule/gRNA molecule complex isgreater than a thermostability value of the reference molecule or thethermostability reference value. For example, in certain embodiments,the Cas9 molecule/gRNA molecule complex may be determined to be stableif the thermostability value of the Cas9 molecule/gRNA molecule complexis at least 8° C. greater than a thermostability value of the referencemolecule or the thermostability reference value. In certain embodiments,the reference molecule may be a reference Cas9 molecule in the absenceof a gRNA molecule. In certain embodiments, the methods including a stepto measure a thermostability value may further comprise steps thatinclude measuring an activity value of the Cas9 molecule/gRNA moleculecomplex as described herein.

Also provided herein based on the disclosed experimental results aremethods that include a step of measuring the activity of a Cas9/moleculegRNA molecule complex, which may also be useful in determining thestability of the complex. The methods that may include a step ofmeasuring the activity of a Cas9/molecule gRNA molecule complex include,without limitation, methods of determining the stability of a Cas9molecule/gRNA molecule complex, methods of determining a condition thatpromotes a stable Cas9 molecule/gRNA molecule complex, methods ofscreening for a stable Cas9 molecule/gRNA molecule complex, methods foridentifying an optimal gRNA to form a stable Cas9 molecule/gRNA moleculecomplex, methods of screening for a Cas9 molecule/gRNA molecule complexfor administration to a subject, and methods of selecting a Cas9molecule/gRNA molecule complex for administration to a subject. Incertain embodiments, an activity value of a Cas9 molecule/gRNA moleculecomplex may be detected. Additionally, in certain embodiments, anactivity value of a reference molecule may be detected. In certainembodiments, the Cas9 molecule/gRNA molecule complex may be determinedto be stable if the an activity value of the Cas9 molecule/gRNA moleculecomplex is greater than an activity value of the reference molecule orthe activity reference value. In certain embodiments, the activity thatis being detected may be a binding activity. In certain embodiments, abinding activity may include, without limitation, the ability of thegRNA molecule to remain hybridized to the DNA target, the ability of thegRNA molecule to bind to the Cas9 molecule of the Cas9 molecule/gRNAmolecule complex, or the ability of the gRNA molecule to bind to theCas9 molecule of the Cas9 molecule/gRNA molecule complex. In certainembodiments, a binding value of the molecule may be measured. In certainembodiments, the Cas9 molecule/gRNA molecule complex may be selected ordetermined to be stable if the binding value of the molecule beingevaluated is greater than the binding value of a reference molecule or abinding reference value. In certain embodiments, the activity is acleavage activity. Some examples of a cleavage activity may include,without limitation, any one or more of the ability of a Cas9molecule/gRNA molecule complex to cleave a target, the propensity of acleavage event mediated by a Cas9 molecule/gRNA molecule complex to beresolved by a particular pathway, e.g., HDR or NHEJ, the ability of aCas9 molecule/gRNA molecule complex to modulate a target. In certainembodiments, a cleavage value of the Cas9 molecule/gRNA molecule complexmay be measured. In certain embodiments, the Cas9 molecule/gRNA moleculecomplex may be selected or determined to be stable if the cleavage valueof the Cas9 molecule/gRNA molecule complex is greater than the cleavagevalue of a reference molecule or a cleavage reference value.

The methods disclosed herein may be performed on a plurality of samples.For example, in certain embodiments, the methods may comprise generatinga plurality of samples, each sample comprising a Cas9 molecule/gRNAmolecule complex generated by combining a Cas9 molecule and one of aplurality of gRNA molecules. In certain embodiments, a thermostabilityvalue and/or activity value of the Cas9 molecule/gRNA molecule complexmay be detected in each of the plurality of samples. In certainembodiments, at least one sample comprising the Cas9 molecule/gRNAmolecule complex may be selected from the plurality of samples. Incertain embodiments, the sample comprising the Cas9 molecule/gRNAmolecule complex may be selected based on one or more of (i) acomparison of the T_(m) in the plurality of samples to a T_(m) of areference complex or a pre-determined threshold T_(m), or (ii) arelative ordering of the T_(m) values of the plurality of samples.

In certain embodiments, the methods may comprise generating a pluralityof Cas9 molecule/gRNA molecule complexes, each comprising a Cas9molecule/gRNA molecule complex generated by combining a Cas9 moleculeand one of a plurality of gRNA molecules. In certain embodiments, athermostability value of the Cas9 molecule/gRNA molecule complex may bedetected for each of the plurality of Cas9 molecule/gRNA moleculecomplexes. In certain embodiments, a Cas9 molecule/gRNA molecule complexmay be determined to be stable if the thermostability value of the Cas9molecule/gRNA molecule complex is greater than a thermostability valueof a reference molecule or a thermostability reference value. In certainembodiments, an activity value of the Cas9 molecule/gRNA moleculecomplex may be detected for each of the plurality of Cas9 molecule/gRNAmolecule complexes. In certain embodiments, a Cas9 molecule/gRNAmolecule complex may be determined to be stable if the activity value ofthe Cas9 molecule/gRNA molecule complex is greater than an activityvalue of a reference molecule or an activity reference value.

Also provided herein are non-naturally occurring Cas9 molecule/gRNAmolecule complexes generated using any of the methods disclosed herein.

Provided herein are compositions that may comprise any of the Cas9molecule/gRNA molecule complexes generated using the methods describedherein. For example, the compositions herein may comprise an isolatedcomplex of a Cas9 molecule and a gRNA molecule having a T_(m) at least8° C. greater than a T_(m) of a reference molecule or T_(m) referencevalue selected according to the methods provided herein.

Also provided herein are vector systems comprising a nucleic acidencoding a Cas9 molecule/gRNA molecule complex generated using any ofthe methods described herein.

Provided herein are methods of delivering a Cas9 molecule/gRNA moleculecomplex to a target cell comprising delivering the Cas9 molecule/gRNAmolecule complex generated using any of the methods described herein.

Provided herein based on the disclosed experimental results are methodsfor evaluating, selecting, optimizing, or designing a Cas9 molecule/gRNAmolecule complex or component thereof. In certain embodiments, thesemethods comprise acquiring or determining a stability value (i.e., valuecorrelated with the stability (e.g., thermostability value or activityvalue)) of the Cas9 molecule in a Cas9 molecule/gRNA molecule complex ora preparation thereof. In certain embodiments, the stability value maybe a thermostability value or activity value of the Cas9 molecule in aCas9 molecule/gRNA molecule complex or a preparation thereof. In certainembodiments, the thermostability value may be a T_(m) value ordenaturation temperature value, and in certain embodiments, thethermostability value is acquired or determined using DSF. In certainembodiments, the stability value is acquired for a Cas9 moleculecomplexed with a gRNA molecule. In other embodiments, the stabilityvalue is acquired for a Cas9 molecule in the presence of a gRNAmolecule. In certain embodiments, the stability value is compared to athermostability reference value (i.e., a parameter correlated withthermostability), e.g., T_(m) reference value, or an activity referencevalue (i.e., a parameter correlated with an activity), such as cleavageactivity, e.g., the ability to cleave a target DNA. For example, whereinthe stability value is the T_(m) value, the T_(m) value may be comparedto a T_(m) reference value to determine whether the T_(m) value isidentical to, greater than, or less than the T_(m) reference value.

In certain embodiments, the methods disclosed herein are used to selector design an optimal Cas9 molecule/gRNA pairing, e.g., a pairing withmaximum stability or with a stability falling within a desired targetrange. In certain embodiments, the method is used to select or designone or more gRNAs for pairing with a particular Cas9 molecule, e.g.,identifying gRNA molecules that complex with a particular Cas9 moleculewith the greatest stability. In other embodiments, the method is used toselect a Cas9 molecule for pairing with a particular gRNA or set ofgRNAs, e.g., identifying Cas9 molecules that complex with a particulargRNA(s) with the greatest stability. In still other embodiments, themethod is used to select both a Cas9 molecule and a gRNA or set of gRNAsfor pairing in a Cas9 molecule/gRNA molecule complex.

Provided herein in certain embodiments are Cas9 molecule/gRNA complexes,or components thereof, exhibiting a desired value correlated with thestability of the Cas9 molecule in the complex, as well as compositionsand pharmaceutical formulations comprising these complexes or componentsthereof. In certain embodiments, this value may be the T_(m) ordenaturation temperature, and in certain embodiments the value isacquired or determined using DSF. In certain of these embodiments, thecomplexes are generated using the methods provided herein.

Provided herein in certain embodiments are methods comprising comparingthe thermostability value. In certain embodiments, the methods comprisecomparing the thermostability value with a thermostability referencevalue. In certain embodiments, the thermostability reference valuecomprises a preselected numerical value (where a value can be a singlenumber or a range), e.g., a preselected numerical value forthermostability, e.g., T_(m) value. In certain embodiments, thethermostability reference value may be a value correlated withthermostability of a) a reference Cas9 molecule, e.g., the same Cas9molecule as the Cas9 molecule in the complex being evaluated (or adifferent Cas9 molecule), in the absence of a gRNA molecule; b) areference Cas9 molecule (e.g., the same Cas9 molecule as the Cas9molecule in the complex being evaluated) complexed with a second gRNAmolecule (i.e., a gRNA other than the one in the complex beingevaluated); or c) a reference Cas9 molecule/gRNA molecule complex,wherein the reference Cas9 molecule/gRNA molecule was formed underdifferent conditions, e.g., with different proportions of Cas9 moleculeand gRNA molecule, than the Cas9 molecule/gRNA molecule complex, or wasformed in a different buffer.

Provided herein in certain embodiments are reference Cas9 molecules. Incertain embodiments, the reference Cas9 molecule may be the same as theCas9 molecule of the complex being evaluated. In certain embodiments,the reference Cas9 molecule may be different, e.g., differs in primarysequence, from the Cas9 molecule of the complex being evaluated. Incertain embodiments, the gRNA molecule of a reference Cas9 molecule/gRNAmolecule complex may be the same as the gRNA molecule of the complexbeing evaluated. In certain embodiments, the gRNA molecule of areference Cas9 molecule/gRNA molecule complex may be different from thegRNA molecule, e.g., differs in sequence or differs by a modification.

Provided herein in certain embodiments, delta values (e.g., a deltavalue is the difference or shift between two values) may be acquired,e.g., determined. In certain embodiments, the delta values may include avalue correlated with the difference in stability of the Cas9molecule/gRNA molecule complex being evaluated and a reference value. Incertain embodiments, the delta value may include a value correlatedwith: the difference in stability, e.g., denaturation temperature orT_(m), of the Cas9 molecule/gRNA molecule complex being evaluated; andthe stability, e.g., denaturation temperature or T_(m) of a referencevalue, e.g., the value for a reference Cas9 molecule/gRNA moleculecomplex.

Provided herein in certain embodiments, the methods may include a stepof comparing the delta value with a delta reference value (e.g., areference value for the delta value). In certain embodiments, this mayinclude evaluating if the delta value is equal to or less than the deltareference value; equal to or greater than the delta reference value; oris within a predetermined range of the delta reference value.

Provided herein in certain embodiments, the methods may includeselecting the Cas9 molecule/gRNA molecule complex (or a componentthereof). In certain embodiments, the method may include selecting theCas9 molecule/gRNA molecule complex (or a component thereof) based on acomparison of a value of a Cas9 molecule/gRNA molecule complex (e.g.,including, but not limited to a thermostability value (e.g., T_(m)value), activity value, or delta value to a reference value. In certainembodiments, the reference value may be, including but not limited to, apredetermined threshold, an upperbound value, a target value. In certainembodiments, the value may be a delta value. In certain embodiments, thereference value may be a delta reference value.

In certain embodiments, the methods may include evaluating if the deltavalue is: equal to or less than the delta reference value; equal to orgreater than the delta reference value; is within a predetermined rangeof the delta reference value.

In certain embodiments, the methods may also include evaluating ormeasuring an activity or property of the selected Cas9 molecule/gRNAmolecule complex (or a component thereof). In certain embodiments, theactivity may be a cleavage activity, e.g., the ability to cleave. Incertain embodiments, the activity may be the ability to be successfullydelivered. In certain embodiments, the activity may be a bindingactivity, e.g., the ability of the gRNA molecule to remain hybridized tothe DNA target.

In certain embodiments, the evaluating step may include evaluating ormeasuring the activity of the selected Cas9 molecule/gRNA moleculecomplex (or component thereof) in a system, such an in vitro system, anex vivo system, or an in vivo system, and assay, such as a cellularassay, or a model, such as a cellular or animal model.

In certain embodiments, the evaluating step may include evaluating ormeasuring an activity of a selected Cas9 molecule/gRNA molecule complex(or component thereof). In certain embodiments, the activity may be acleavage activity, such as the ability to induce indels, the ability tomodify a target DNA, the propensity of a preselected repair method,e.g., a pathway described herein, e.g., HDR or NHEJ, to mediate acleavage event catalyzed by the Cas9 molecule/gRNA molecule complex. Incertain embodiments, the activity may be a binding activity, such as theability of the gRNA molecule to remain hybridized to the DNA target.

In certain embodiments, the methods may include selecting a Cas9molecule/gRNA molecule complex (or component thereof) for an activity.For example, the activity may be a cleavage activity such as the abilityto induce indels; the ability to modify a target DNA; the propensity ofa preselected repair method, e.g., a pathway described herein, e.g., HDRor NHEJ, to mediate a cleavage event catalyzed by the Cas9 molecule/gRNAmolecule complex. In certain embodiments, the activity may be a bindingactivity, such as the ability of the gRNA molecule to remain hybridizedto the DNA target.

In certain embodiments, the methods may include designing or optimizinga Cas9 molecule/gRNA molecule complex (or component thereof) for anactivity. For example, the activity may be a cleavage activity such asthe ability to induce indels; the ability to modify a target DNA; thepropensity of a preselected repair method, e.g., a pathway describedherein, e.g., HDR or NHEJ, to mediate a cleavage event catalyzed by theCas9 molecule/gRNA molecule complex. In certain embodiments, theactivity may be a binding activity, such as the ability of the gRNAmolecule to remain hybridized to the DNA target.

In certain embodiments, the method may include determining the stabilityof the Cas9 molecule of at least X Cas9 molecule/gRNA moleculecomplexes. In certain embodiments, X may be equal to 2, 3, 4, 5, 10, 20,30, 40, 50, 100, 500, or 1,000. In certain embodiments, determining thestability may include measuring the stability value of the Cas 9molecule. In certain embodiments, the stability value may be thethermostability value. In certain embodiments, the thermostability valuemay be the T_(m) value. In certain embodiments, the T_(m) value may bedetermined by DSF.

In certain embodiments, determining stability may comprise determiningthe temperature at which the Cas9 molecule of a Cas9 molecule/gRNAmolecule complex denatures, e.g., determining the T_(m) value. Incertain embodiments, the T_(m) value may be determined by DSF.

In certain embodiments, the methods may comprise determining by DSF, thetemperature at which the Cas9 molecule of a Cas9 molecule/gRNA moleculecomplex denatures, e.g., determining the T_(m) value, for a first Cas9molecule/gRNA molecule complex and a second Cas9 molecule/gRNA moleculecomplex.

In certain embodiments, a first Cas9 molecule/gRNA molecule complex anda second Cas9 molecule/gRNA molecule complex of the at least X Cas9molecule/gRNA molecule complexes differ by having Cas9 molecules ofdifferent sequence, having gRNA molecules that differ in sequence or bymodification, by capping or tailing, having been formed under differentconditions, e.g., different stoichiometries.

In certain embodiments, responsive to the determination of stability, aCas9 molecule/gRNA molecule complex (or a component there of) may beselected for optimized or preselected delivery characteristics, e.g.,wherein delivery comprises delivery by RNP cationic lipid transfection,a viral vector (e.g., AAV), or RNA transfection.

In certain embodiments, responsive to the determination of stability, aCas9 molecule/gRNA molecule complex (or a component there of) isselected for optimized or preselected relationship with a qualitycontrol standard.

In certain embodiments, responsive to the determination of stability, aCas9 molecule/gRNA molecule complex (or a component thereof) may beselected as meeting a quality control or release standard.

In certain embodiments, methods herein may comprise selecting a Cas9molecule/gRNA molecule complex (or a component thereof) if athermostability value, e.g, a T_(m) value or denaturation temperaturevalue, or a delta value, has a preselected relationship with a referencevalue or a delta reference value.

In certain embodiments, responsive to the determination of stability, aCas9 molecule/gRNA molecule complex (or a component thereof) is selectedfor optimized or preselected characteristic, e.g., a cleavagecharacteristic.

In certain embodiments, responsive to evaluation of a delta valuebetween a thermostability value for a Cas9 molecule/gRNA moleculecomplex and a thermostability value of a reference molecule, e.g., Cas9molecule in the absence of gRNA molecule, a Cas9 molecule/gRNA moleculecomplex (or a component there of) is selected.

In certain embodiments, responsive to evaluation of a delta valuebetween an activity value for a Cas9 molecule/gRNA molecule complex andan activity value of a reference molecule, e.g., Cas9 molecule in theabsence of gRNA molecule, a Cas9 molecule/gRNA molecule complex (or acomponent there of) is selected.

In certain embodiments, methods herein may comprise evaluating a libraryof (or a single) candidate gRNA molecules, e.g., a library of tracrRNAmolecules or sequences, complexed with a Cas9 molecule, and responsiveto the determination of stability of a Cas9 molecule/candidate gRNAmolecule complex, selecting a candidate gRNA molecule or sequence, e.g.,a candidate tracr gRNA molecule or sequence.

In certain embodiments, the library may comprise tracr RNA molecules orsequences of differing structure, e.g., differing length, differingsequence, or having different modifications, e.g., having additionalphosphate groups or alternative 5′ cap structures.

In certain embodiments, the tracr RNA molecule or sequences may bedisposed on a chimeric gRNA.

In certain embodiments, the method s herein may comprise evaluating acomponent for inclusion in a Cas9 molecule/gRNA molecule preparation,comprising evaluating the stability of the Cas9 molecule of the Cas9molecule/gRNA molecule complex in a preparation comprising thecomponent. In certain embodiments, the component may comprise anadditive, a small molecule, a stabilizing reagent, buffer, pH, saltconcentration, glycerol concentration, or other buffer component.

In certain embodiments, the methods herein may comprise evaluating acandidate Cas 9 molecule for inclusion in a Cas9 molecule/gRNA moleculecomplex, comprising evaluating the stability of the Cas9 molecule of theCas9 molecule/gRNA molecule complex. In certain embodiments, thecandidate Cas9 molecule may comprise a chimeric Cas9 molecule, or asynthetic or engineered Cas9 molecule, e.g., a Cas9 molecule with aportion or portions deleted.

In certain embodiments, determining stability may comprise, determiningby differential scanning fluorimetry (DSF), the temperature at which theCas9 molecule of a Cas9 molecule/gRNA molecule complex denatures, e.g.,the T_(m), of the Cas9 molecule.

Provided herein are reaction mixtures. The reaction mixtures maycomprise a Cas9 molecule/gRNA molecule complex, e.g., a Cas9molecule/gRNA molecule complex described herein; and a signal emittingcompound, e.g., a dye, wherein signal emission is correlated todenaturation of the Cas9 molecule.

Provided herein are differential scanning fluorimeters having disposedtherein: a Cas9 molecule/gRNA molecule complex; and a signal emittingcompound, e.g., a dye, wherein signal emission is correlated todenaturation of the Cas9 molecule.

Provided herein are Cas9 molecule/gRNA molecule complexes evaluated,selected, optimized, or designed by a method described herein.

Provided herein are compositions comprising a Cas9 molecule/gRNAmolecule complex selected or designed by a method described herein. Incertain embodiments, the compositions may be a pharmaceuticalcomposition. In certain embodiments, the Cas9 molecule/gRNA moleculecomplex may be formulated in a pharmaceutically acceptable carrier.

As discussed herein the methods disclosed herein may be used toevaluate, select or design a complex optimized for formulation ordelivery. For example, methods described herein can be used in multipleways for improving complex formation of a chimeric gRNA or a tracrRNAwith a Cas9 molecule (e.g., a Cas9 protein) using any delivery methodsuch as, but not limited to, RNP cationic lipid transfection, viralvectors (e.g., AAV), or RNA transfections.

Methods discussed herein can be used for quality control, or todetermine if a release standard has been met for both protein and RNAcomponents. For example, if a standard for a thermal shift is not met,e.g., where there is no thermal shift when incubating Cas9 protein withRNA, a Cas9 molecule or a gRNA molecule of insufficient quality isindicated. In an embodiment, the method is used as a guide, or as aprocess control, to address such issues, e.g., by the detection andremoval of impurities.

Methods described herein can be used for assessing libraries ofcandidate Cas9 molecules or candidate gRNA molecules for use in aCas9/gRNA complex. In an embodiment, the method identifies componentsfor optimized binding. This can allow screening of candidates tooptimized target cleavage, or other properties. Methods described hereincan also be used to evaluate modifications in the length andcompositions of gRNA. For example, after purifying a mutant Cas9protein, a library of gRNA molecules (e.g., tracrRNA molecules) orsequences can be incubated with the protein at a preselected ratio,e.g., at a minimum 1:1 ratio of RNA:protein. The appearance of a thermalshift observed when compared to the Cas9 protein in the absence of agRNA molecule is indicative of an effective gRNA molecule, e.g., a gRNAmolecule capable of mediating one or more CRISPR/Cas-related activitiesin vitro, ex vivo, or in vivo.

The methods described herein can be used to screen a library of gRNAmolecules (e.g., tracrRNA molecules) or sequences having tracr-regionsof different length, combined with cognate guide sequences fused withdifferent linker sequences and assayed for binding using DSF. Well boundcomplexes could be screened for cutting activity in vitro. Methodsdescribed herein allow for the evaluation of chemical modifications ofRNA, additional phosphate groups, or alternative 5′ cap structures, foreffect on cleavage, suitability for delivery or other characteristicsdiscussed herein.

The methods described herein can be used to screen a library ofcomponents, such as additives, small molecule stabilizing reagents,buffers, salt, e.g., salt molarity, glycerol concentration, and otherbuffer components for stabilizing the interaction of a Cas9 molecule anda gRNA molecule.

The methods described herein can be used to screen a library ofchimeric, engineered, or synthetic Cas9 molecules, e.g., chimeric orengineered Cas9 molecules for stabilizing the interaction of Cas9molecule and gRNA molecule. Insufficient thermal shift is indicativethat RNA binding is sub-optimal or disrupted. A partial thermal shiftwould imply that the RNA is binding productively. For chimeric orengineered Cas9 molecules which have no DSF T_(m), libraries of gRNAmolecules (e.g., tracrRNA molecules) or sequences can be screened forrestoring binding, as measured by DSF.

A Cas9 molecule perceived as inactive can be used in a thermostabilityassay against a nucleic acid molecule library, e.g., a randomizednucleic acid library. This will allow screening for novel molecules thatcan fulfill the role of tracrRNA. Using this newly discovered nucleicacid molecule (e.g., tracrRNA molecule) one can develop new gRNAs totarget genomic DNA, in vivo RNA, and/or genetic material from invasiveorganisms and viruses.

The methods described herein can be applied to any mutated and chimericforms of Cas9 molecule. It is also understood that the methods describedherein can be applied to other Cas molecules, e.g., other Cas moleculesdescribed herein.

Guide RNA (gRNA) Molecules

A gRNA molecule, as that term is used herein, refers to a nucleic acidthat promotes the specific targeting or homing of a gRNA molecule/Cas9molecule complex to a target nucleic acid. gRNA molecules can beunimolecular (having a single RNA molecule), sometimes referred toherein as “chimeric” gRNAs, or modular (comprising more than one, andtypically two, separate RNA molecules). The gRNA molecules providedherein comprise a targeting domain comprising, consisting of, orconsisting essentially of a nucleic acid sequence fully or partiallycomplementary to a target nucleic acid sequence. In certain embodiments,the gRNA molecule further comprises one or more additional domains,including for example a first complementarity domain, a linking domain,a second complementarity domain, a proximal domain, a tail domain,and/or a 5′ extension domain. Each of these domains is discussed indetail below. In certain embodiments, one or more of the domains in thegRNA molecule comprises an amino acid sequence identical to or sharingsequence homology with a naturally occurring sequence, e.g., from S.pyogenes, S. aureus, or S. thermophilus.

Several exemplary gRNA structures are provided in FIGS. 1A-1I. Withregard to the three-dimensional form, or intra- or inter-strandinteractions of an active form of a gRNA, regions of highcomplementarity are sometimes shown as duplexes in FIGS. 1A-1I and otherdepictions provided herein. FIG. 7 illustrates gRNA domain nomenclatureusing the gRNA sequence of SEQ ID NO:42, which contains one hairpin loopin the tracrRNA-derived region. In certain embodiments, a gRNA maycontain more than one (e.g., two, three, or more) hairpin loops in thisregion (see, e.g., FIGS. 1H-1I).

In certain embodiments, a unimolecular, or chimeric, gRNA comprises,preferably from 5′ to 3′:

-   -   a targeting domain comprising, consisting of, or consisting        essentially of a nucleic acid sequence fully or partially        complementary to a target nucleic acid sequence;    -   a first complementarity domain;    -   a linking domain;    -   a second complementarity domain (which is complementary to the        first complementarity domain);    -   a proximal domain; and    -   optionally, a tail domain.

In certain embodiments, a modular gRNA comprises:

-   -   a first strand comprising, preferably from 5′ to 3′:        -   a targeting domain comprising, consisting of, or consisting            essentially of a nucleic acid sequence fully or partially            complementary to a target nucleic acid sequence; and        -   a first complementarity domain; and    -   a second strand, comprising, preferably from 5′ to 3′:        -   optionally, a 5′ extension domain;        -   a second complementarity domain;        -   a proximal domain; and        -   optionally, a tail domain.

Targeting Domain

The targeting domain (sometimes referred to alternatively as the guidesequence or complementarity region) comprises, consists of, or consistsessentially of a nucleic acid sequence that is complementary orpartially complementary to a target nucleic acid. The nucleic acidsequence to which all or a portion of the targeting domain iscomplementary or partially complementary is referred to herein as thetarget domain. Methods for selecting targeting domains are known in theart (see, e.g., Fu 2014; Sternberg 2014).

The strand of the target nucleic acid comprising the target domain isreferred to herein as the complementary strand because it iscomplementary to the targeting domain sequence. Since the targetingdomain is part of a gRNA molecule, it comprises the base uracil (U)rather than thymine (T); conversely, any DNA molecule encoding the gRNAmolecule will comprise thymine rather than uracil. In a targetingdomain/target domain pair, the uracil bases in the targeting domain willpair with the adenine bases in the target domain. In certainembodiments, the degree of complementarity between the targeting domainand target domain is sufficient to allow targeting of a gRNAmolecule/Cas9 molecule complex to the target nucleic acid.

In certain embodiments, the targeting domain comprises a core domain andan optional secondary domain. In certain of these embodiments, the coredomain is located 3′ to the secondary domain, and in certain of theseembodiments the core domain is located at or near the 3′ end of thetargeting domain. In certain of these embodiments, the core domainconsists of or consists essentially of about 8 to about 13 nucleotidesat the 3′ end of the targeting domain. In certain embodiments, only thecore domain is complementary or partially complementary to thecorresponding portion of the target domain, and in certain of theseembodiments the core domain is fully complementary to the correspondingportion of the target domain. In other embodiments, the secondary domainis also complementary or partially complementary to a portion of thetarget domain. In certain embodiments, the core domain is complementaryor partially complementary to a core domain target in the target domain,while the secondary domain is complementary or partially complementaryto a secondary domain target in the target domain. In certainembodiments, the core domain and secondary domain have the same degreeof complementarity with their respective corresponding portions of thetarget domain. In other embodiments, the degree of complementaritybetween the core domain and its target and the degree of complementaritybetween the secondary domain and its target may differ. In certain ofthese embodiments, the core domain may have a higher degree ofcomplementarity for its target than the secondary domain, whereas inother embodiments the secondary domain may have a higher degree ofcomplementarity than the core domain.

In certain embodiments, the targeting domain and/or the core domainwithin the targeting domain is 3 to 100, 5 to 100, 10 to 100, or 20 to100 nucleotides in length, and in certain of these embodiments thetargeting domain or core domain is 3 to 15, 3 to 20, 5 to 20, 10 to 20,15 to 20, 5 to 50, 10 to 50, or 20 to 50 nucleotides in length. Incertain embodiments, the targeting domain and/or the core domain withinthe targeting domain is 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,19, 20, 21, 22, 23, 24, 25, or 26 nucleotides in length. In certainembodiments, the targeting domain and/or the core domain within thetargeting domain is 6+/−2, 7+/−2, 8+/−2, 9+/−2, 10+/−2, 10+/−4, 10+/−5,11+/−2, 12+/−2, 13+/−2, 14+/−2, 15+/−2, or 16+−2, 20+/−5, 30+/−5,40+/−5, 50+/−5, 60+/−5, 70+/−5, 80+/−5, 90+/−5, or 100+/−5 nucleotidesin length.

In certain embodiments wherein the targeting domain includes a coredomain, the core domain is 3 to 20 nucleotides in length, and in certainof these embodiments the core domain 5 to 15 or 8 to 13 nucleotides inlength. In certain embodiments wherein the targeting domain includes asecondary domain, the secondary domain is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14 or 15 nucleotides in length. In certain embodimentswherein the targeting domain comprises a core domain that is 8 to 13nucleotides in length, the targeting domain is 26, 25, 24, 23, 22, 21,20, 19, 18, 17, or 16 nucleotides in length, and the secondary domain is13 to 18, 12 to 17, 11 to 16, 10 to 15, 9 to 14, 8 to 13, 7 to 12, 6 to11, 5 to 10, 4 to 9, or 3 to 8 nucleotides in length, respectively.

In certain embodiments, the targeting domain is fully complementary tothe target domain. Likewise, where the targeting domain comprises a coredomain and/or a secondary domain, in certain embodiments one or both ofthe core domain and the secondary domain are fully complementary to thecorresponding portions of the target domain. In other embodiments, thetargeting domain is partially complementary to the target domain, and incertain of these embodiments where the targeting domain comprises a coredomain and/or a secondary domain, one or both of the core domain and thesecondary domain are partially complementary to the correspondingportions of the target domain. In certain of these embodiments, thenucleic acid sequence of the targeting domain, or the core domain ortargeting domain within the targeting domain, is at least 80, 85, 90, or95% complementary to the target domain or to the corresponding portionof the target domain. In certain embodiments, the targeting domainand/or the core or secondary domains within the targeting domain includeone or more nucleotides that are not complementary with the targetdomain or a portion thereof, and in certain of these embodiments thetargeting domain and/or the core or secondary domains within thetargeting domain include 1, 2, 3, 4, 5, 6, 7, or 8 nucleotides that arenot complementary with the target domain. In certain embodiments, thecore domain includes 1, 2, 3, 4, or 5 nucleotides that are notcomplementary with the corresponding portion of the target domain. Incertain embodiments wherein the targeting domain includes one or morenucleotides that are not complementary with the target domain, one ormore of said non-complementary nucleotides are located within fivenucleotides of the 5′ or 3′ end of the targeting domain. In certain ofthese embodiments, the targeting domain includes 1, 2, 3, 4, or 5nucleotides within five nucleotides of its 5′ end, 3′ end, or both its5′ and 3′ ends that are not complementary to the target domain. Incertain embodiments wherein the targeting domain includes two or morenucleotides that are not complementary to the target domain, two or moreof said non-complementary nucleotides are adjacent to one another, andin certain of these embodiments the two or more consecutivenon-complementary nucleotides are located within five nucleotides of the5′ or 3′ end of the targeting domain. In other embodiments, the two ormore consecutive non-complementary nucleotides are both located morethan five nucleotides from the 5′ and 3′ ends of the targeting domain.

In certain embodiments, the targeting domain, core domain, and/orsecondary domain do not comprise any modifications. In otherembodiments, the targeting domain, core domain, and/or secondary domain,or one or more nucleotides therein, have a modification, including butnot limited to the modifications set forth below. In certainembodiments, one or more nucleotides of the targeting domain, coredomain, and/or secondary domain may comprise a 2′ modification (e.g., amodification at the 2′ position on ribose), e.g., a 2-acetylation, e.g.,a 2′ methylation. In certain embodiments, the backbone of the targetingdomain can be modified with a phosphorothioate. In certain embodiments,modifications to one or more nucleotides of the targeting domain, coredomain, and/or secondary domain render the targeting domain and/or thegRNA comprising the targeting domain less susceptible to degradation ormore bio-compatible, e.g., less immunogenic. In certain embodiments, thetargeting domain and/or the core or secondary domains include 1, 2, 3,4, 5, 6, 7, or 8 or more modifications, and in certain of theseembodiments the targeting domain and/or core or secondary domainsinclude 1, 2, 3, or 4 modifications within five nucleotides of theirrespective 5′ ends and/or 1, 2, 3, or 4 modifications within fivenucleotides of their respective 3′ ends. In certain embodiments, thetargeting domain and/or the core or secondary domains comprisemodifications at two or more consecutive nucleotides.

In certain embodiments wherein the targeting domain includes core andsecondary domains, the core and secondary domains contain the samenumber of modifications. In certain of these embodiments, both domainsare free of modifications. In other embodiments, the core domainincludes more modifications than the secondary domain, or vice versa.

In certain embodiments, modifications to one or more nucleotides in thetargeting domain, including in the core or secondary domains, areselected to not interfere with targeting efficacy, which can beevaluated by testing a candidate modification using a system as setforth below. gRNAs having a candidate targeting domain having a selectedlength, sequence, degree of complementarity, or degree of modificationcan be evaluated using a system as set forth below. The candidatetargeting domain can be placed, either alone or with one or more othercandidate changes in a gRNA molecule/Cas9 molecule system known to befunctional with a selected target, and evaluated.

In certain embodiments, all of the modified nucleotides arecomplementary to and capable of hybridizing to corresponding nucleotidespresent in the target domain. In another embodiment, 1, 2, 3, 4, 5, 6,7, or 8 or more modified nucleotides are not complementary to or capableof hybridizing to corresponding nucleotides present in the targetdomain.

FIGS. 1A-1I provide examples of the placement of the targeting domainwithin a gRNA molecule.

First and Second Complementarity Domains

The first and second complementarity (sometimes referred toalternatively as the crRNA-derived hairpin sequence and tracrRNA-derivedhairpin sequences, respectively) domains are fully or partiallycomplementary to one another. In certain embodiments, the degree ofcomplementarity is sufficient for the two domains to form a duplexedregion under at least some physiological conditions. In modular gRNAmolecules, the two molecules are associated by virtue of thehybridization of the complementarity domains (see e.g., FIG. 1A). Incertain embodiments, the degree of complementarity between the first andsecond complementarity domains, together with other properties of thegRNA, is sufficient to allow targeting of a Cas9 molecule to a targetnucleic acid. Examples of first and second complementarity domains areset forth in FIGS. 1A-1G.

In certain embodiments (see, e.g., FIGS. 1A-1B) the first and/or secondcomplementarity domain includes one or more nucleotides that lackcomplementarity with the corresponding complementarity domain. Incertain embodiments, the first and/or second complementarity domainincludes 1, 2, 3, 4, 5, or 6 nucleotides that do not complement with thecorresponding complementarity domain. For example, the secondcomplementarity domain may contain 1, 2, 3, 4, 5, or 6 nucleotides thatdo not pair with corresponding nucleotides in the first complementaritydomain. In certain embodiments, the nucleotides on the first or secondcomplementarity domain that do not complement with the correspondingcomplementarity domain loop out from the duplex formed between the firstand second complementarity domains. In certain of these embodiments, theunpaired loop-out is located on the second complementarity domain, andin certain of these embodiments the unpaired region begins 1, 2, 3, 4,5, or 6 nucleotides from the 5′ end of the second complementaritydomain.

In certain embodiments, the first complementarity domain is 5 to 30, 5to 25, 7 to 25, 5 to 24, 5 to 23, 7 to 22, 5 to 22, 5 to 21, 5 to 20, 7to 18, 7 to 15, 9 to 16, or 10 to 14 nucleotides in length, and incertain of these embodiments the first complementarity domain is 5, 6,7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or25 nucleotides in length. In certain embodiments, the secondcomplementarity domain is 5 to 27, 7 to 27, 7 to 25, 5 to 24, 5 to 23, 5to 22, 5 to 21, 7 to 20, 5 to 20, 7 to 18, 7 to 17, 9 to 16, or 10 to 14nucleotides in length, and in certain of these embodiments the secondcomplementarity domain is 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, or 26 nucleotides in length. In certainembodiments, the first and second complementarity domains are eachindependently 6+/−2, 7+/−2, 8+/−2, 9+/−2, 10+/−2, 11+/−2, 12+/−2,13+/−2, 14+/−2, 15+/−2, 16+/−2, 17+/−2, 18+/−2, 19+/−2, or 20+/−2,21+/−2, 22+/−2, 23+/−2, or 24+/−2 nucleotides in length. In certainembodiments, the second complementarity domain is longer than the firstcomplementarity domain, e.g., 2, 3, 4, 5, or 6 nucleotides longer.

In certain embodiments, the first and/or second complementarity domainseach independently comprise three subdomains, which, in the 5′ to 3′direction are: a 5′ subdomain, a central subdomain, and a 3′ subdomain.In certain embodiments, the 5′ subdomain and 3′ subdomain of the firstcomplementarity domain are fully or partially complementary to the 3′subdomain and 5′ subdomain, respectively, of the second complementaritydomain.

In certain embodiments, the 5′ subdomain of the first complementaritydomain is 4 to 9 nucleotides in length, and in certain of theseembodiments the 5′ domain is 4, 5, 6, 7, 8, or 9 nucleotides in length.In certain embodiments, the 5′ subdomain of the second complementaritydomain is 3 to 25, 4 to 22, 4 to 18, or 4 to 10 nucleotides in length,and in certain of these embodiments the 5′ domain is 3, 4, 5, 6, 7, 8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25nucleotides in length. In certain embodiments, the central subdomain ofthe first complementarity domain is 1, 2, or 3 nucleotides in length. Incertain embodiments, the central subdomain of the second complementaritydomain is 1, 2, 3, 4, or 5 nucleotides in length. In certainembodiments, the 3′ subdomain of the first complementarity domain is 3to 25, 4 to 22, 4 to 18, or 4 to 10 nucleotides in length, and incertain of these embodiments the 3′ subdomain is 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25nucleotides in length. In certain embodiments, the 3′ subdomain of thesecond complementarity domain is 4 to 9, e.g., 4, 5, 6, 7, 8, or 9nucleotides in length.

The first and/or second complementarity domains can share homology with,or be derived from, naturally occurring or reference first and/or secondcomplementarity domains. In certain of these embodiments, the firstand/or second complementarity domains have at least 50%, 60%, 70%, 80%,85%, 90%, or 95% homology with, or differ by no more than 1, 2, 3, 4, 5,or 6 nucleotides from, the naturally occurring or reference first and/orsecond complementarity domain. In certain of these embodiments, thefirst and/or second complementarity domains may have at least 50%, 60%,70%, 80%, 85%, 90%, or 95% homology with homology with a first and/orsecond complementarity domain from S. pyogenes or S. aureus.

In certain embodiments, the first and/or second complementarity domainsdo not comprise any modifications. In other embodiments, the firstand/or second complementarity domains or one or more nucleotides thereinhave a modification, including but not limited to a modification setforth below. In certain embodiments, one or more nucleotides of thefirst and/or second complementarity domain may comprise a 2′modification (e.g., a modification at the 2′ position on ribose), e.g.,a 2-acetylation, e.g., a 2′ methylation. In certain embodiments, thebackbone of the targeting domain can be modified with aphosphorothioate. In certain embodiments, modifications to one or morenucleotides of the first and/or second complementarity domain render thefirst and/or second complementarity domain and/or the gRNA comprisingthe first and/or second complementarity less susceptible to degradationor more bio-compatible, e.g., less immunogenic. In certain embodiments,the first and/or second complementarity domains each independentlyinclude 1, 2, 3, 4, 5, 6, 7, or 8 or more modifications, and in certainof these embodiments the first and/or second complementarity domainseach independently include 1, 2, 3, or 4 modifications within fivenucleotides of their respective 5′ ends, 3′ ends, or both their 5′ and3′ ends. In other embodiments, the first and/or second complementaritydomains each independently contain no modifications within fivenucleotides of their respective 5′ ends, 3′ ends, or both their 5′ and3′ ends. In certain embodiments, one or both of the first and secondcomplementarity domains comprise modifications at two or moreconsecutive nucleotides.

In certain embodiments, modifications to one or more nucleotides in thefirst and/or second complementarity domains are selected to notinterfere with targeting efficacy, which can be evaluated by testing acandidate modification in the system set forth below. gRNAs having acandidate first or second complementarity domain having a selectedlength, sequence, degree of complementarity, or degree of modificationcan be evaluated using a system as set forth below. The candidatecomplementarity domain can be placed, either alone or with one or moreother candidate changes in a gRNA molecule/Cas9 molecule system known tobe functional with a selected target, and evaluated.

In certain embodiments, the duplexed region formed by the first andsecond complementarity domains is, for example, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 21, or 22 bp in length, excluding anylooped out or unpaired nucleotides.

In certain embodiments, the first and second complementarity domains,when duplexed, comprise 11 paired nucleotides (see, for e.g., gRNA ofSEQ ID NO:48). In certain embodiments, the first and secondcomplementarity domains, when duplexed, comprise 15 paired nucleotides(see, e.g., gRNA of SEQ ID NO:50). In certain embodiments, the first andsecond complementarity domains, when duplexed, comprise 16 pairednucleotides (see, e.g., gRNA of SEQ ID NO:51). In certain embodiments,the first and second complementarity domains, when duplexed, comprise 21paired nucleotides (see, e.g., gRNA of SEQ ID NO:29).

In certain embodiments, one or more nucleotides are exchanged betweenthe first and second complementarity domains to remove poly-U tracts.For example, nucleotides 23 and 48 or nucleotides 26 and 45 of the gRNAof SEQ ID NO:48 may be exchanged to generate the gRNA of SEQ ID NOs:49or 31, respectively. Similarly, nucleotides 23 and 39 of the gRNA of SEQID NO:29 may be exchanged with nucleotides 50 and 68 to generate thegRNA of SEQ ID NO:30.

Linking Domain

The linking domain is disposed between and serves to link the first andsecond complementarity domains in a unimolecular or chimeric gRNA. FIGS.1B-1E provide examples of linking domains. In certain embodiments, partof the linking domain is from a crRNA-derived region, and another partis from a tracrRNA-derived region.

In certain embodiments, the linking domain links the first and secondcomplementarity domains covalently. In certain of these embodiments, thelinking domain consists of or comprises a covalent bond. In otherembodiments, the linking domain links the first and secondcomplementarity domains non-covalently. In certain embodiments, thelinking domain is ten or fewer nucleotides in length, e.g., 1, 2, 3, 4,5, 6, 7, 8, 9, or 10 nucleotides. In other embodiments, the linkingdomain is greater than 10 nucleotides in length, e.g., 11, 12, 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 or more nucleotides. Incertain embodiments, the linking domain is 2 to 50, 2 to 40, 2 to 30, 2to 20, 2 to 10, 2 to 5, 10 to 100, 10 to 90, 10 to 80, 10 to 70, 10 to60, 10 to 50, 10 to 40, 10 to 30, 10 to 20, 10 to 15, 20 to 100, 20 to90, 20 to 80, 20 to 70, 20 to 60, 20 to 50, 20 to 40, 20 to 30, or 20 to25 nucleotides in length. In certain embodiments, the linking domain is10+/−5, 20+/−5, 20+/−10, 30+/−5, 30+/−10, 40+/−5, 40+/−10, 50+/−5,50+/−10, 60+/−5, 60+/−10, 70+/−5, 70+/−10, 80+/−5, 80+/−10, 90+/−5,90+/−10, 100+/−5, or 100+/−10 nucleotides in length.

In certain embodiments, the linking domain shares homology with, or isderived from, a naturally occurring sequence, e.g., the sequence of atracrRNA that is 5′ to the second complementarity domain. In certainembodiments, the linking domain has at least 50%, 60%, 70%, 80%, 90%, or95% homology with or differs by no more than 1, 2, 3, 4, 5, or 6nucleotides from a linking domain disclosed herein, e.g., the linkingdomains of FIGS. 1B-1E.

In certain embodiments, the linking domain does not comprise anymodifications. In other embodiments, the linking domain or one or morenucleotides therein have a modification, including but not limited tothe modifications set forth below. In certain embodiments, one or morenucleotides of the linking domain may comprise a 2′ modification (e.g.,a modification at the 2′ position on ribose), e.g., a 2-acetylation,e.g., a 2′ methylation. In certain embodiments, the backbone of thelinking domain can be modified with a phosphorothioate. In certainembodiments, modifications to one or more nucleotides of the linkingdomain render the linking domain and/or the gRNA comprising the linkingdomain less susceptible to degradation or more bio-compatible, e.g.,less immunogenic. In certain embodiments, the linking domain includes 1,2, 3, 4, 5, 6, 7, or 8 or more modifications, and in certain of theseembodiments the linking domain includes 1, 2, 3, or 4 modificationswithin five nucleotides of its 5′ and/or 3′ end. In certain embodiments,the linking domain comprises modifications at two or more consecutivenucleotides.

In certain embodiments, modifications to one or more nucleotides in thelinking domain are selected to not interfere with targeting efficacy,which can be evaluated by testing a candidate modification using asystem as set forth below. gRNAs having a candidate linking domainhaving a selected length, sequence, degree of complementarity, or degreeof modification can be evaluated in a system as set forth below. Thecandidate linking domain can be placed, either alone or with one or moreother candidate changes in a gRNA molecule/Cas9 molecule system known tobe functional with a selected target, and evaluated.

In certain embodiments, the linking domain comprises a duplexed region,typically adjacent to or within 1, 2, or 3 nucleotides of the 3′ end ofthe first complementarity domain and/or the 5′ end of the secondcomplementarity domain. In certain of these embodiments, the duplexedregion of the linking region is 10+/−5, 15+/−5, 20+/−5, 20+/−10, or30+/−5 bp in length. In certain embodiments, the duplexed region of thelinking domain is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15bp in length. In certain embodiments, the sequences forming the duplexedregion of the linking domain are fully complementarity. In otherembodiments, one or both of the sequences forming the duplexed regioncontain one or more nucleotides (e.g., 1, 2, 3, 4, 5, 6, 7, or 8nucleotides) that are not complementary with the other duplex sequence.

5′ Extension Domain

In certain embodiments, a modular gRNA as disclosed herein comprises a5′ extension domain, i.e., one or more additional nucleotides 5′ to thesecond complementarity domain (see, e.g., FIG. 1A). In certainembodiments, the 5′ extension domain is 2 to 10 or more, 2 to 9, 2 to 8,2 to 7, 2 to 6, 2 to 5, or 2 to 4 nucleotides in length, and in certainof these embodiments the 5′ extension domain is 2, 3, 4, 5, 6, 7, 8, 9,or 10 or more nucleotides in length.

In certain embodiments, the 5′ extension domain nucleotides do notcomprise modifications, e.g., modifications of the type provided below.However, in certain embodiments, the 5′ extension domain comprises oneor more modifications, e.g., modifications that it render it lesssusceptible to degradation or more bio-compatible, e.g., lessimmunogenic. By way of example, the backbone of the 5′ extension domaincan be modified with a phosphorothioate, or other modification(s) as setforth below. In certain embodiments, a nucleotide of the 5′ extensiondomain can comprise a 2′ modification (e.g., a modification at the 2′position on ribose), e.g., a 2-acetylation, e.g., a 2′ methylation, orother modification(s) as set forth below.

In certain embodiments, the 5′ extension domain can comprise as many as1, 2, 3, 4, 5, 6, 7, or 8 modifications. In certain embodiments, the 5′extension domain comprises as many as 1, 2, 3, or 4 modifications within5 nucleotides of its 5′ end, e.g., in a modular gRNA molecule. Incertain embodiments, the 5′ extension domain comprises as many as 1, 2,3, or 4 modifications within 5 nucleotides of its 3′ end, e.g., in amodular gRNA molecule.

In certain embodiments, the 5′ extension domain comprises modificationsat two consecutive nucleotides, e.g., two consecutive nucleotides thatare within 5 nucleotides of the 5′ end of the 5′ extension domain,within 5 nucleotides of the 3′ end of the 5′ extension domain, or morethan 5 nucleotides away from one or both ends of the 5′ extensiondomain. In certain embodiments, no two consecutive nucleotides aremodified within 5 nucleotides of the 5′ end of the 5′ extension domain,within 5 nucleotides of the 3′ end of the 5′ extension domain, or withina region that is more than 5 nucleotides away from one or both ends ofthe 5′ extension domain. In certain embodiments, no nucleotide ismodified within 5 nucleotides of the 5′ end of the 5′ extension domain,within 5 nucleotides of the 3′ end of the 5′ extension domain, or withina region that is more than 5 nucleotides away from one or both ends ofthe 5′ extension domain.

Modifications in the 5′ extension domain can be selected so as to notinterfere with gRNA molecule efficacy, which can be evaluated by testinga candidate modification in a system as set forth below. gRNAs having acandidate 5′ extension domain having a selected length, sequence, degreeof complementarity, or degree of modification, can be evaluated in asystem as set forth below. The candidate 5′ extension domain can beplaced, either alone, or with one or more other candidate changes in agRNA molecule/Cas9 molecule system known to be functional with aselected target and evaluated.

In certain embodiments, the 5′ extension domain has at least 60, 70, 80,85, 90 or 95% homology with, or differs by no more than 1, 2, 3, 4, 5,or 6 nucleotides from, a reference 5′ extension domain, e.g., anaturally occurring, e.g., an S. pyogenes, S. aureus, or S.thermophilus, 5′ extension domain, or a 5′ extension domain describedherein, e.g., from FIGS. 1A-1G.

Proximal Domain

FIGS. 1A-1G provide examples of proximal domains.

In certain embodiments, the proximal domain is 5 to 20 or morenucleotides in length, e.g., 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, 20, 21, 22, 23, 24, 25, or 26 nucleotides in length. Incertain of these embodiments, the proximal domain is 6+/−2, 7+/−2,8+/−2, 9+/−2, 10+/−2, 11+/−2, 12+/−2, 13+/−2, 14+/−2, 14+/−2, 16+/−2,17+/−2, 18+/−2, 19+/−2, or 20+/−2 nucleotides in length. In certainembodiments, the proximal domain is 5 to 20, 7, to 18, 9 to 16, or 10 to14 nucleotides in length.

In certain embodiments, the proximal domain can share homology with orbe derived from a naturally occurring proximal domain. In certain ofthese embodiments, the proximal domain has at least 50%, 60%, 70%, 80%,85%, 90%, or 95% homology with or differs by no more than 1, 2, 3, 4, 5,or 6 nucleotides from a proximal domain disclosed herein, e.g., an S.pyogenes, S. aureus, or S. thermophilus proximal domain, including thoseset forth in FIGS. 1A-1G.

In certain embodiments, the proximal domain does not comprise anymodifications. In other embodiments, the proximal domain or one or morenucleotides therein have a modification, including but not limited tothe modifications set forth in herein. In certain embodiments, one ormore nucleotides of the proximal domain may comprise a 2′ modification(e.g., a modification at the 2′ position on ribose), e.g., a2-acetylation, e.g., a 2′ methylation. In certain embodiments, thebackbone of the proximal domain can be modified with a phosphorothioate.In certain embodiments, modifications to one or more nucleotides of theproximal domain render the proximal domain and/or the gRNA comprisingthe proximal domain less susceptible to degradation or morebio-compatible, e.g., less immunogenic. In certain embodiments, theproximal domain includes 1, 2, 3, 4, 5, 6, 7, or 8 or moremodifications, and in certain of these embodiments the proximal domainincludes 1, 2, 3, or 4 modifications within five nucleotides of its 5′and/or 3′ end. In certain embodiments, the proximal domain comprisesmodifications at two or more consecutive nucleotides.

In certain embodiments, modifications to one or more nucleotides in theproximal domain are selected to not interfere with targeting efficacy,which can be evaluated by testing a candidate modification in a systemas set forth below. gRNAs having a candidate proximal domain having aselected length, sequence, degree of complementarity, or degree ofmodification can be evaluated in a system as set forth below. Thecandidate proximal domain can be placed, either alone or with one ormore other candidate changes in a gRNA molecule/Cas9 molecule systemknown to be functional with a selected target, and evaluated.

Tail Domain

A broad spectrum of tail domains are suitable for use in the gRNAmolecules disclosed herein. FIGS. 1A and 1C-1G provide examples of suchtail domains.

In certain embodiments, the tail domain is absent. In other embodiments,the tail domain is 1 to 100 or more nucleotides in length, e.g., 1, 2,3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100nucleotides in length. In certain embodiments, the tail domain is 1 to5, 1 to 10, 1 to 15, 1 to 20, 1 to 50, 10 to 100, 20 to 100, 10 to 90,20 to 90, 10 to 80, 20 to 80, 10 to 70, 20 to 70, 10 to 60, 20 to 60, 10to 50, 20 to 50, 10 to 40, 20 to 40, 10 to 30, 20 to 30, 20 to 25, 10 to20, or 10 to 15 nucleotides in length. In certain embodiments, the taildomain is 5+/−5, 10+/−5, 20+/−10, 20+/−5, 25+/−10, 30+/−10, 30+/−5,40+/−10, 40+/−5, 50+/−10, 50+/−5, 60+/−10, 60+/−5, 70+/−10, 70+/−5,80+/−10, 80+/−5, 90+/−10, 90+/−5, 100+/−10, or 100+/−5 nucleotides inlength.

In certain embodiments, the tail domain can share homology with or bederived from a naturally occurring tail domain or the 5′ end of anaturally occurring tail domain. In certain of these embodiments, theproximal domain has at least 50%, 60%, 70%, 80%, 85%, 90%, or 95%homology with or differs by no more than 1, 2, 3, 4, 5, or 6 nucleotidesfrom a naturally occurring tail domain disclosed herein, e.g., an S.pyogenes, S. aureus, or S. thermophilus tail domain, including those setforth in FIGS. 1A and 1C-1G.

In certain embodiments, the tail domain includes sequences that arecomplementary to each other and which, under at least some physiologicalconditions, form a duplexed region. In certain of these embodiments, thetail domain comprises a tail duplex domain which can form a tailduplexed region. In certain embodiments, the tail duplexed region is 3,4, 5, 6, 7, 8, 9, 10, 11, or 12 bp in length. In certain embodiments,the tail domain comprises a single stranded domain 3′ to the tail duplexdomain that does not form a duplex. In certain of these embodiments, thesingle stranded domain is 3 to 10 nucleotides in length, e.g., 3, 4, 5,6, 7, 8, 9, 10, or 4 to 6 nucleotides in length.

In certain embodiments, the tail domain does not comprise anymodifications. In other embodiments, the tail domain or one or morenucleotides therein have a modification, including but not limited tothe modifications set forth herein. In certain embodiments, one or morenucleotides of the tail domain may comprise a 2′ modification (e.g., amodification at the 2′ position on ribose), e.g., a 2-acetylation, e.g.,a 2′ methylation. In certain embodiments, the backbone of the taildomain can be modified with a phosphorothioate. In certain embodiments,modifications to one or more nucleotides of the tail domain render thetail domain and/or the gRNA comprising the tail domain less susceptibleto degradation or more bio-compatible, e.g., less immunogenic. Incertain embodiments, the tail domain includes 1, 2, 3, 4, 5, 6, 7, or 8or more modifications, and in certain of these embodiments the taildomain includes 1, 2, 3, or 4 modifications within five nucleotides ofits 5′ and/or 3′ end. In certain embodiments, the tail domain comprisesmodifications at two or more consecutive nucleotides.

In certain embodiments, modifications to one or more nucleotides in thetail domain are selected to not interfere with targeting efficacy, whichcan be evaluated by testing a candidate modification as set forth below.gRNAs having a candidate tail domain having a selected length, sequence,degree of complementarity, or degree of modification can be evaluatedusing a system as set forth below. The candidate tail domain can beplaced, either alone or with one or more other candidate changes in agRNA molecule/Cas9 molecule system known to be functional with aselected target, and evaluated.

In certain embodiments, the tail domain includes nucleotides at the 3′end that are related to the method of in vitro or in vivo transcription.When a T7 promoter is used for in vitro transcription of the gRNA, thesenucleotides may be any nucleotides present before the 3′ end of the DNAtemplate. When a U6 promoter is used for in vivo transcription, thesenucleotides may be the sequence UUUUUU. When an H1 promoter is used fortranscription, these nucleotides may be the sequence UUUU. Whenalternate pol-III promoters are used, these nucleotides may be variousnumbers of uracil bases depending on, e.g., the termination signal ofthe pol-III promoter, or they may include alternate bases.

In certain embodiments, the proximal and tail domain taken togethercomprise, consist of, or consist essentially of the sequence set forthin SEQ ID NOs:32, 33, 34, 35, 36, or 37.

Exemplary Unimolecular Chimeric gRNAs

In certain embodiments, a unimolecular or chimeric gRNA as disclosedherein has the structure: 5′ [targeting domain]-[first complementaritydomain]-[linking domain]-[second complementarity domain]-[proximaldomain]-[tail domain]-3′, wherein:

the targeting domain comprises a core domain and optionally a secondarydomain, and is 10 to 50 nucleotides in length;

the first complementarity domain is 5 to 25 nucleotides in length and,in certain embodiments has at least 50, 60, 70, 80, 85, 90, or 95%homology with a reference first complementarity domain disclosed herein;

the linking domain is 1 to 5 nucleotides in length;

the second complementarity domain is 5 to 27 nucleotides in length and,in certain embodiments has at least 50, 60, 70, 80, 85, 90, or 95%homology with a reference second complementarity domain disclosedherein;

the proximal domain is 5 to 20 nucleotides in length and, in certainembodiments has at least 50, 60, 70, 80, 85, 90, or 95% homology with areference proximal domain disclosed herein; and

the tail domain is absent or a nucleotide sequence is 1 to 50nucleotides in length and, in certain embodiments has at least 50, 60,70, 80, 85, 90, or 95% homology with a reference tail domain disclosedherein.

In certain embodiments, a unimolecular gRNA as disclosed hereincomprises, preferably from 5′ to 3′:

-   -   a targeting domain, e.g., comprising 10-50 nucleotides;    -   a first complementarity domain, e.g., comprising 15, 16, 17, 18,        19, 20, 21, 22, 23, 24, 25, or 26 nucleotides;    -   a linking domain;    -   a second complementarity domain;    -   a proximal domain; and    -   a tail domain,

wherein,

-   -   (a) the proximal and tail domain, when taken together, comprise        at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53        nucleotides;    -   (b) there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49,        50, or 53 nucleotides 3′ to the last nucleotide of the second        complementarity domain; or    -   (c) there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50,        51, or 54 nucleotides 3′ to the last nucleotide of the second        complementarity domain that is complementary to its        corresponding nucleotide of the first complementarity domain.

In certain embodiments, the sequence from (a), (b), and/or (c) has atleast 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% homology with thecorresponding sequence of a naturally occurring gRNA, or with a gRNAdescribed herein.

In certain embodiments, the proximal and tail domain, when takentogether, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50,or 53 nucleotides.

In certain embodiments, there are at least 15, 18, 20, 25, 30, 31, 35,40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of thesecond complementarity domain.

In certain embodiments, there are at least 16, 19, 21, 26, 31, 32, 36,41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of thesecond complementarity domain that are complementary to thecorresponding nucleotides of the first complementarity domain.

In certain embodiments, the targeting domain consists of, consistsessentially of, or comprises 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or26 nucleotides (e.g., 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26consecutive nucleotides) complementary or partially complementary to thetarget domain or a portion thereof, e.g., the targeting domain is 16,17, 18, 19, 20, 21, 22, 23, 24, 25, or 26 nucleotides in length. Incertain of these embodiments, the targeting domain is complementary tothe target domain over the entire length of the targeting domain, theentire length of the target domain, or both.

In certain embodiments, a unimolecular or chimeric gRNA moleculedisclosed herein (comprising a targeting domain, a first complementarydomain, a linking domain, a second complementary domain, a proximaldomain and, optionally, a tail domain) comprises the amino acid sequenceset forth in SEQ ID NO:42, wherein the targeting domain is listed as 20Ns (residues 1-20) but may range in length from 16 to 26 nucleotides andwherein the final six residues (residues 97-102) represent a terminationsignal for the U6 promoter but may be absent or fewer in number. Incertain embodiments, the unimolecular, or chimeric, gRNA molecule is aS. pyogenes gRNA molecule.

In certain embodiments, a unimolecular or chimeric gRNA moleculedisclosed herein (comprising a targeting domain, a first complementarydomain, a linking domain, a second complementary domain, a proximaldomain and, optionally, a tail domain) comprises the amino acid sequenceset forth in SEQ ID NO:38, wherein the targeting domain is listed as 20Ns (residues 1-20) but may range in length from 16 to 26 nucleotides,and wherein the final six residues (residues 97-102) represent atermination signal for the U6 promoter but may be absent or fewer innumber. In certain embodiments, the unimolecular or chimeric gRNAmolecule is an S. aureus gRNA molecule.

The sequences and structures of exemplary chimeric gRNAs are also shownin FIGS. 1H-1I.

Exemplary Modular gRNAs

In certain embodiments, a modular gRNA disclosed herein comprises:

-   -   a first strand comprising, preferably from 5′ to 3′;        -   a targeting domain, e.g., comprising 15, 16, 17, 18, 19, 20,            21, 22, 23, 24, 25, or 26 nucleotides;        -   a first complementarity domain; and    -   a second strand, comprising, preferably from 5′ to 3′:        -   optionally a 5′ extension domain;        -   a second complementarity domain;        -   a proximal domain; and        -   a tail domain,

wherein:

-   -   (a) the proximal and tail domain, when taken together, comprise        at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53        nucleotides;    -   (b) there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49,        50, or 53 nucleotides 3′ to the last nucleotide of the second        complementarity domain; or    -   (c) there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50,        51, or 54 nucleotides 3′ to the last nucleotide of the second        complementarity domain that is complementary to its        corresponding nucleotide of the first complementarity domain.

In certain embodiments, the sequence from (a), (b), or (c), has at least60, 75, 80, 85, 90, 95, or 99% homology with the corresponding sequenceof a naturally occurring gRNA, or with a gRNA described herein.

In certain embodiments, the proximal and tail domain, when takentogether, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50,or 53 nucleotides.

In certain embodiments, there are at least 15, 18, 20, 25, 30, 31, 35,40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of thesecond complementarity domain.

In certain embodiments, there are at least 16, 19, 21, 26, 31, 32, 36,41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of thesecond complementarity domain that is complementary to its correspondingnucleotide of the first complementarity domain.

In certain embodiments, the targeting domain comprises, has, or consistsof, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26 nucleotides (e.g., 16,17, 18, 19, 20, 21, 22, 23, 24, 25, or 26 consecutive nucleotides)having complementarity with the target domain, e.g., the targetingdomain is 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26 nucleotides inlength.

In certain embodiments, the targeting domain consists of, consistsessentially of, or comprises 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or26 nucleotides (e.g., 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26consecutive nucleotides) complementary to the target domain or a portionthereof. In certain of these embodiments, the targeting domain iscomplementary to the target domain over the entire length of thetargeting domain, the entire length of the target domain, or both.

In certain embodiments, the targeting domain comprises, consists of, orconsists essentially of 16 nucleotides (e.g., 16 consecutivenucleotides) having complementarity with the target domain, e.g., thetargeting domain is 16 nucleotides in length. In certain embodiments ofthese embodiments, (a) the proximal and tail domain, when takentogether, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50,or 53 nucleotides; (b) there are at least 15, 18, 20, 25, 30, 31, 35,40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of thesecond complementarity domain; and/or (c) there are at least 16, 19, 21,26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the lastnucleotide of the second complementarity domain that is complementary toits corresponding nucleotide of the first complementarity domain.

In certain embodiments, the targeting domain comprises, consists of, orconsists essentially of 17 nucleotides (e.g., 17 consecutivenucleotides) having complementarity with the target domain, e.g., thetargeting domain is 17 nucleotides in length. In certain of theseembodiments, (a) the proximal and tail domain, when taken together,comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53nucleotides; (b) there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45,49, 50, or 53 nucleotides 3′ to the last nucleotide of the secondcomplementarity domain; and/or (c) there are at least 16, 19, 21, 26,31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotideof the second complementarity domain that is complementary to itscorresponding nucleotide of the first complementarity domain.

In certain embodiments, the targeting domain comprises, consists of, orconsists essentially of 18 nucleotides (e.g., 18 consecutivenucleotides) having complementarity with the target domain, e.g., thetargeting domain is 18 nucleotides in length. In certain of theseembodiments, (a) the proximal and tail domain, when taken together,comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53nucleotides; (b) there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45,49, 50, or 53 nucleotides 3′ to the last nucleotide of the secondcomplementarity domain; and/or (c) there are at least 16, 19, 21, 26,31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotideof the second complementarity domain that is complementary to itscorresponding nucleotide of the first complementarity domain.

In certain embodiments, the targeting domain comprises, consists of, orconsists essentially of 19 nucleotides (e.g., 19 consecutivenucleotides) having complementarity with the target domain, e.g., thetargeting domain is 19 nucleotides in length. In certain of theseembodiments, (a) the proximal and tail domain, when taken together,comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53nucleotides; (b) there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45,49, 50, or 53 nucleotides 3′ to the last nucleotide of the secondcomplementarity domain; and/or (c) there are at least 16, 19, 21, 26,31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotideof the second complementarity domain that is complementary to itscorresponding nucleotide of the first complementarity domain.

In certain embodiments, the targeting domain comprises, consists of, orconsists essentially of 20 nucleotides (e.g., 20 consecutivenucleotides) having complementarity with the target domain, e.g., thetargeting domain is 20 nucleotides in length. In certain of theseembodiments, (a) the proximal and tail domain, when taken together,comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53nucleotides; (b) there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45,49, 50, or 53 nucleotides 3′ to the last nucleotide of the secondcomplementarity domain; and/or (c) there are at least 16, 19, 21, 26,31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotideof the second complementarity domain that is complementary to itscorresponding nucleotide of the first complementarity domain.

In certain embodiments, the targeting domain comprises, consists of, orconsists essentially of 21 nucleotides (e.g., 21 consecutivenucleotides) having complementarity with the target domain, e.g., thetargeting domain is 21 nucleotides in length. In certain of theseembodiments, (a) the proximal and tail domain, when taken together,comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53nucleotides; (b) there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45,49, 50, or 53 nucleotides 3′ to the last nucleotide of the secondcomplementarity domain; and/or (c) there are at least 16, 19, 21, 26,31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotideof the second complementarity domain that is complementary to itscorresponding nucleotide of the first complementarity domain.

In certain embodiments, the targeting domain comprises, consists of, orconsists essentially of 22 nucleotides (e.g., 22 consecutivenucleotides) having complementarity with the target domain, e.g., thetargeting domain is 22 nucleotides in length. In certain of theseembodiments, (a) the proximal and tail domain, when taken together,comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53nucleotides; (b) there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45,49, 50, or 53 nucleotides 3′ to the last nucleotide of the secondcomplementarity domain; and/or (c) there are at least 16, 19, 21, 26,31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotideof the second complementarity domain that is complementary to itscorresponding nucleotide of the first complementarity domain.

In certain embodiments, the targeting domain comprises, consists of, orconsists essentially of 23 nucleotides (e.g., 23 consecutivenucleotides) having complementarity with the target domain, e.g., thetargeting domain is 23 nucleotides in length. In certain of theseembodiments, (a) the proximal and tail domain, when taken together,comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53nucleotides; (b) there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45,49, 50, or 53 nucleotides 3′ to the last nucleotide of the secondcomplementarity domain; and/or (c) there are at least 16, 19, 21, 26,31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotideof the second complementarity domain that is complementary to itscorresponding nucleotide of the first complementarity domain.

In certain embodiments, the targeting domain comprises, consists of, orconsists essentially of 24 nucleotides (e.g., 24 consecutivenucleotides) having complementarity with the target domain, e.g., thetargeting domain is 24 nucleotides in length. In certain of theseembodiments, (a) the proximal and tail domain, when taken together,comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53nucleotides; (b) there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45,49, 50, or 53 nucleotides 3′ to the last nucleotide of the secondcomplementarity domain; and/or (c) there are at least 16, 19, 21, 26,31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotideof the second complementarity domain that is complementary to itscorresponding nucleotide of the first complementarity domain.

In certain embodiments, the targeting domain comprises, consists of, orconsists essentially of 25 nucleotides (e.g., 25 consecutivenucleotides) having complementarity with the target domain, e.g., thetargeting domain is 25 nucleotides in length. In certain of theseembodiments, (a) the proximal and tail domain, when taken together,comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53nucleotides; (b) there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45,49, 50, or 53 nucleotides 3′ to the last nucleotide of the secondcomplementarity domain; and/or (c) there are at least 16, 19, 21, 26,31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotideof the second complementarity domain that is complementary to itscorresponding nucleotide of the first complementarity domain.

In certain embodiments, the targeting domain comprises, consists of, orconsists essentially of 26 nucleotides (e.g., 26 consecutivenucleotides) having complementarity with the target domain, e.g., thetargeting domain is 26 nucleotides in length. In certain of theseembodiments, (a) the proximal and tail domain, when taken together,comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53nucleotides; (b) there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45,49, 50, or 53 nucleotides 3′ to the last nucleotide of the secondcomplementarity domain; and/or there are at least 16, 19, 21, 26, 31,32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide ofthe second complementarity domain that is complementary to itscorresponding nucleotide of the first complementarity domain.

Methods for Designing gRNAs

Methods for designing gRNAs are described herein, including methods forselecting, designing, and validating targeting domains for use in thegRNAs described herein. Exemplary targeting domains for incorporationinto gRNAs are also provided herein. It is contemplated herein that incertain embodiments the targeting domain hybridizes to the target domainthrough complementary base pairing.

Methods for selection and validation of target sequences as well asoff-target analyses have been described previously (see, e.g., Mali2013; Hsu 2013; Fu 2014; Heigwer 2014; Bae 2014; Xiao 2014). Forexample, a software tool can be used to optimize the choice of potentialtargeting domains corresponding to a user's target sequence, e.g., tominimize total off-target activity across the genome. Off-targetactivity may be other than cleavage. For each possible targeting domainchoice using S. pyogenes Cas9, the tool can identify all off-targetsequences (preceding either NAG or NGG PAMs) across the genome thatcontain up to certain number (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) ofmismatched base-pairs. The cleavage efficiency at each off-targetsequence can be predicted, e.g., using an experimentally-derivedweighting scheme. Each possible targeting domain is then rankedaccording to its total predicted off-target cleavage; the top-rankedtargeting domains represent those that are likely to have the greateston-target cleavage and the least off-target cleavage. Other functions,e.g, automated reagent design for CRISPR construction, primer design forthe on-target Surveyor assay, and primer design for high-throughputdetection and quantification of off-target cleavage via next-gensequencing, can also be included in the tool. Candidate targetingdomains and gRNAs comprising those targeting domains can be functionallyevaluated using methods known in the art and/or as set forth herein.

As a non-limiting example, targeting domains for use in gRNAs for usewith S. pyogenes and S. aureus Cas9s were identified using a DNAsequence searching algorithm. gRNA design was carried out using customgRNA design software based on the public tool cas-offinder (Bae 2014).This software scores guides after calculating their genome-wideoff-target propensity. Typically matches ranging from perfect matches to7 mismatches are considered for guides ranging in length from 17 to 24.Once the off-target sites are computationally determined, an aggregatescore is calculated for each guide and summarized in a tabular outputusing a web-interface. In addition to identifying potential target sitesadjacent to PAM sequences, the software also identifies all PAM adjacentsequences that differ by 1, 2, 3, or more than 3 nucleotides from theselected target sites. Genomic DNA sequences for each gene were obtainedfrom the UCSC Genome browser, and sequences were screened for repeatelements using the publically available RepeaT_(m)asker program.RepeaT_(m)asker searches input DNA sequences for repeated elements andregions of low complexity. The output is a detailed annotation of therepeats present in a given query sequence.

Following identification, targeting domain were ranked into tiers basedon their orthogonality and the presence of a 5′ G (based onidentification of close matches in the human genome containing arelevant PAM, e.g., an NGG PAM for S. pyogenes, or an NNGRRT (SEQ IDNO:204) or NNGRRV (SEQ ID NO:205) PAM for S. aureus). Orthogonalityrefers to the number of sequences in the human genome that contain aminimum number of mismatches to the target sequence. A “high level oforthogonality” or “good orthogonality” may, for example, refer to 20-mertargeting domain that have no identical sequences in the human genomebesides the intended target, nor any sequences that contain one or twomismatches in the target sequence. Targeting domains with goodorthogonality are selected to minimize off-target DNA cleavage.

Targeting domains were identified for both single-gRNA nuclease cleavageand for a dual-gRNA paired “nickase” strategy. Criteria for selectingtargeting domains and the determination of which targeting domains canbe used for the dual-gRNA paired “nickase” strategy is based on twoconsiderations:

-   -   (1) Targeting domain pairs should be oriented on the DNA such        that PAMs are facing out and cutting with the D10A Cas9 nickase        will result in 5′ overhangs; and    -   (2) An assumption that cleaving with dual nickase pairs will        result in deletion of the entire intervening sequence at a        reasonable frequency. However, cleaving with dual nickase pairs        can also result in indel mutations at the site of only one of        the gRNAs. Candidate pair members can be tested for how        efficiently they remove the entire sequence versus causing indel        mutations at the target site of one targeting domain.

Cas9 Molecules

Cas9 molecules of a variety of species can be used in the methods andcompositions described herein. While S. pyogenes, S. aureus, and S.thermophilus Cas9 molecules are the subject of much of the disclosureherein, Cas9 molecules of, derived from, or based on the Cas9 proteinsof other species listed herein can be used as well. These include, forexample, Cas9 molecules from Acidovorax avenae, Actinobacilluspleuropneumoniae, Actinobacillus succinogenes, Actinobacillus suis,Actinomyces sp., cycliphilus denitrificans, Aminomonas paucivorans,Bacillus cereus, Bacillus smithii, Bacillus thuringiensis, Bacteroidessp., Blastopirellula marina, Bradyrhizobium sp., Brevibacilluslaterosporus, Campylobacter coli, Campylobacter jejuni, Campylobacterlari, Candidatus puniceispirillum, Clostridium cellulolyticum,Clostridium perfringens, Corynebacterium accolens, Corynebacteriumdiphtheria, Corynebacterium matruchotii, Dinoroseobacter shibae,Eubacterium dolichum, gamma proteobacterium, Gluconacetobacterdiazotrophicus, Haemophilus parainfluenzae, Haemophilus sputorum,Helicobacter canadensis, Helicobacter cinaedi, Helicobacter mustelae,Ilyobacter polytropus, Kingella kingae, Lactobacillus crispatus,Listeria ivanovii, Listeria monocytogenes, Listeriaceae bacterium,Methylocystis sp., Methylosinus trichosporium, Mobiluncus mulieris,Neisseria bacilliformis, Neisseria cinerea, Neisseria flavescens,Neisseria lactamica, Neisseria sp., Neisseria wadsworthii, Nitrosomonassp., Parvibaculum lavamentivorans, Pasteurella multocida,Phascolarctobacterium succinatutens, Ralstonia syzygii, Rhodopseudomonaspalustris, Rhodovulum sp., Simonsiella muelleri, Sphingomonas sp.,Sporolactobacillus vineae, Staphylococcus lugdunensis, Streptococcussp., Subdoligranulum sp., Tistrella mobilis, Treponema sp., orVerminephrobacter eiseniae.

Cas9 Domains

Crystal structures have been determined for two different naturallyoccurring bacterial Cas9 molecules (Jinek 2014) and for S. pyogenes Cas9with a guide RNA (e.g., a synthetic fusion of crRNA and tracrRNA)(Nishimasu 2014; Anders 2014).

A naturally occurring Cas9 molecule comprises two lobes: a recognition(REC) lobe and a nuclease (NUC) lobe; each of which further comprisedomains described herein. FIGS. 8A-8B provide a schematic of theorganization of important Cas9 domains in the primary structure. Thedomain nomenclature and the numbering of the amino acid residuesencompassed by each domain used throughout this disclosure is asdescribed previously (Nishimasu 2014). The numbering of the amino acidresidues is with reference to Cas9 from S. pyogenes.

The REC lobe comprises the arginine-rich bridge helix (BH), the REC1domain, and the REC2 domain. The REC lobe does not share structuralsimilarity with other known proteins, indicating that it is aCas9-specific functional domain. The BH domain is a long a helix andarginine rich region and comprises amino acids 60-93 of S. pyogenes Cas9(SEQ ID NO:2). The REC1 domain is important for recognition of therepeat:anti-repeat duplex, e.g., of a gRNA or a tracrRNA, and istherefore critical for Cas9 activity by recognizing the target sequence.The REC1 domain comprises two REC1 motifs at amino acids 94 to 179 and308 to 717 of S. pyogenes Cas9 (SEQ ID NO:2). These two REC1 domains,though separated by the REC2 domain in the linear primary structure,assemble in the tertiary structure to form the REC1 domain. The REC2domain, or parts thereof, may also play a role in the recognition of therepeat:anti-repeat duplex. The REC2 domain comprises amino acids 180-307of S. pyogenes Cas9 (SEQ ID NO:2).

The NUC lobe comprises the RuvC domain, the HNH domain, and thePAM-interacting (PI) domain. The RuvC domain shares structuralsimilarity to retroviral integrase superfamily members and cleaves asingle strand, e.g., the non-complementary strand of the target nucleicacid molecule. The RuvC domain is assembled from the three split RuvCmotifs (RuvCI, RuvCII, and RuvCIII, which are often commonly referred toin the art as RuvCI domain or N-terminal RuvC domain, RuvCII domain, andRuvCIII domain, respectively) at amino acids 1-59, 718-769, and909-1098, respectively, of S. pyogenes Cas9 (SEQ ID NO:2). Similar tothe REC1 domain, the three RuvC motifs are linearly separated by otherdomains in the primary structure. However, in the tertiary structure,the three RuvC motifs assemble and form the RuvC domain. The HNH domainshares structural similarity with HNH endonucleases and cleaves a singlestrand, e.g., the complementary strand of the target nucleic acidmolecule. The HNH domain lies between the RuvC II-III motifs andcomprises amino acids 775-908 of S. pyogenes Cas9 (SEQ ID NO:2). The PIdomain interacts with the PAM of the target nucleic acid molecule, andcomprises amino acids 1099-1368 of S. pyogenes Cas9 (SEQ ID NO:2).

RuvC-Like Domain and HNH-Like Domain

In certain embodiments, a Cas9 molecule or Cas9 polypeptide comprises anHNH-like domain and a RuvC-like domain, and in certain of theseembodiments cleavage activity is dependent on the RuvC-like domain andthe HNH-like domain. A Cas9 molecule or Cas9 polypeptide can compriseone or more of a RuvC-like domain and an HNH-like domain. In certainembodiments, a Cas9 molecule or Cas9 polypeptide comprises a RuvC-likedomain, e.g., a RuvC-like domain described below, and/or an HNH-likedomain, e.g., an HNH-like domain described below.

RuvC-Like Domains

In certain embodiments, a RuvC-like domain cleaves a single strand,e.g., the non-complementary strand of the target nucleic acid molecule.The Cas9 molecule or Cas9 polypeptide can include more than oneRuvC-like domain (e.g., one, two, three or more RuvC-like domains). Incertain embodiments, a RuvC-like domain is at least 5, 6, 7, 8 aminoacids in length but not more than 20, 19, 18, 17, 16 or 15 amino acidsin length. In certain embodiments, the Cas9 molecule or Cas9 polypeptidecomprises an N-terminal RuvC-like domain of about 10 to 20 amino acids,e.g., about 15 amino acids in length.

N-Terminal RuvC-Like Domains

Some naturally occurring Cas9 molecules comprise more than one RuvC-likedomain with cleavage being dependent on the N-terminal RuvC-like domain.Accordingly, a Cas9 molecule or Cas9 polypeptide can comprise anN-terminal RuvC-like domain. Exemplary N-terminal RuvC-like domains aredescribed below.

In certain embodiments, a Cas9 molecule or Cas9 polypeptide comprises anN-terminal RuvC-like domain comprising an amino acid sequence of FormulaI:

(SEQ ID NO: 20) D-X₁-G-X₂-X₃-X₄-X₅-G-X₆-X₇-X₈-X₉,

wherein

X₁ is selected from I, V, M, L, and T (e.g., selected from I, V, and L);

X₂ is selected from T, I, V, S, N, Y, E, and L (e.g., selected from T,V, and I);

X₃ is selected from N, S, G, A, D, T, R, M, and F (e.g., A or N);

X₄ is selected from S, Y, N, and F (e.g., S);

X₅ is selected from V, I, L, C, T, and F (e.g., selected from V, I andL);

X₆ is selected from W, F, V, Y, S, and L (e.g., W);

X₇ is selected from A, S, C, V, and G (e.g., selected from A and S);

X₈ is selected from V, I, L, A, M, and H (e.g., selected from V, I, Mand L); and

X₉ is selected from any amino acid or is absent (e.g., selected from T,V, I, L, A, F, S, A, Y, M, and R, or, e.g., selected from T, V, I, L,and A).

In certain embodiments, the N-terminal RuvC-like domain differs from asequence of SEQ ID NO:20 by as many as 1 but no more than 2, 3, 4, or 5residues.

In certain embodiments, the N-terminal RuvC-like domain is cleavagecompetent. In other embodiments, the N-terminal RuvC-like domain iscleavage incompetent.

In certain embodiments, a Cas9 molecule or Cas9 polypeptide comprises anN-terminal RuvC-like domain comprising an amino acid sequence of FormulaII:

(SEQ ID NO: 21) D-X₁-G-X₂-X₃-S-X₅-G-X₆-X₇-X₈-X₉,

wherein

X₁ is selected from I, V, M, L, and T (e.g., selected from I, V, and L);

X₂ is selected from T, I, V, S, N, Y, E, and L (e.g., selected from T,V, and I);

X₃ is selected from N, S, G, A, D, T, R, M and F (e.g., A or N);

X₅ is selected from V, I, L, C, T, and F (e.g., selected from V, I andL);

X₆ is selected from W, F, V, Y, S, and L (e.g., W);

X₇ is selected from A, S, C, V, and G (e.g., selected from A and S);

X₈ is selected from V, I, L, A, M, and H (e.g., selected from V, I, Mand L); and

X₉ is selected from any amino acid or is absent (e.g., selected from T,V, I, L, A, F, S, A, Y, M, and R or selected from e.g., T, V, I, L, andA).

In certain embodiments, the N-terminal RuvC-like domain differs from asequence of SEQ ID NO:21 by as many as 1 but not more than 2, 3, 4, or 5residues.

In certain embodiments, the N-terminal RuvC-like domain comprises anamino acid sequence of Formula III:

(SEQ ID NO: 22) D-I-G-X₂-X₃-S-V-G-W-A-X₈-X₉,

wherein

X₂ is selected from T, I, V, S, N, Y, E, and L (e.g., selected from T,V, and I);

X₃ is selected from N, S, G, A, D, T, R, M, and F (e.g., A or N);

X₈ is selected from V, I, L, A, M, and H (e.g., selected from V, I, Mand L); and

X₉ is selected from any amino acid or is absent (e.g., selected from T,V, I, L, A, F, S, A, Y, M, and R or selected from e.g., T, V, I, L, andA).

In certain embodiments, the N-terminal RuvC-like domain differs from asequence of SEQ ID NO:22 by as many as 1 but not more than, 2, 3, 4, or5 residues.

In certain embodiments, the N-terminal RuvC-like domain comprises anamino acid sequence of Formula IV:

(SEQ ID NO: 23) D-I-G-T-N-S-V-G-W-A-V-X,

wherein

X is a non-polar alkyl amino acid or a hydroxyl amino acid, e.g., X isselected from V, I, L, and T (e.g., the Cas9 molecule can comprise anN-terminal RuvC-like domain shown in FIGS. 2A-2G (depicted as Y)).

In certain embodiments, the N-terminal RuvC-like domain differs from asequence of SEQ ID NO:23 by as many as 1 but not more than, 2, 3, 4, or5 residues.

In certain embodiments, the N-terminal RuvC-like domain differs from asequence of an N-terminal RuvC like domain disclosed herein, e.g., inFIGS. 3A-3B, as many as 1 but no more than 2, 3, 4, or 5 residues. In anembodiment, 1, 2, 3 or all of the highly conserved residues identifiedin FIGS. 3A-3B are present.

In certain embodiments, the N-terminal RuvC-like domain differs from asequence of an N-terminal RuvC-like domain disclosed herein, e.g., inFIGS. 4A-4B, as many as 1 but no more than 2, 3, 4, or 5 residues. In anembodiment, 1, 2, or all of the highly conserved residues identified inFIGS. 4A-4B are present.

Additional RuvC-Like Domains

In addition to the N-terminal RuvC-like domain, the Cas9 molecule orCas9 polypeptide can comprise one or more additional RuvC-like domains.In certain embodiments, the Cas9 molecule or Cas9 polypeptide cancomprise two additional RuvC-like domains. Preferably, the additionalRuvC-like domain is at least 5 amino acids in length and, e.g., lessthan 15 amino acids in length, e.g., 5 to 10 amino acids in length,e.g., 8 amino acids in length.

An additional RuvC-like domain can comprise an amino acid sequence ofFormula V:

(SEQ ID NO: 15) I-X₁-X₂-E-X₃-A-R-E,

wherein

X₁ is V or H;

X₂ is I, L or V (e.g., I or V); and

X₃ is M or T.

In certain embodiments, the additional RuvC-like domain comprises anamino acid sequence of Formula VI:

(SEQ ID NO: 16) I-V-X₂-E-M-A-R-E,

wherein

X₂ is I, L or V (e.g., I or V) (e.g., the Cas9 molecule or Cas9polypeptide can comprise an additional RuvC-like domain shown in FIG.2A-2G (depicted as B)).

An additional RuvC-like domain can comprise an amino acid sequence ofFormula VII:

(SEQ ID NO: 17) H-H-A-X₁-D-A-X₂-X₃,

wherein

X₁ is H or L;

X₂ is R or V; and

X₃ is E or V.

In certain embodiments, the additional RuvC-like domain comprises theamino acid sequence: H-H-A-H-D-A-Y-L (SEQ ID NO:18).

In certain embodiments, the additional RuvC-like domain differs from asequence of SEQ ID NOs:15-18 by as many as 1 but not more than 2, 3, 4,or 5 residues.

In certain embodiments, the sequence flanking the N-terminal RuvC-likedomain has the amino acid sequence of Formula VIII:

(SEQ ID NO: 19) K-X₁′-Y-X₂′-X₃′-X₄′-Z-T-D-X₉′-Y,

wherein

X_(1′) is selected from K and P;

X_(2′) is selected from V, L, I, and F (e.g., V, I and L);

X_(3′) is selected from G, A and S (e.g., G);

X_(4′) is selected from L, I, V, and F (e.g., L);

X_(9′) is selected from D, E, N, and Q; and

Z is an N-terminal RuvC-like domain, e.g., as described above.

HNH-Like Domains

In certain embodiments, an HNH-like domain cleaves a single strandedcomplementary domain, e.g., a complementary strand of a double strandednucleic acid molecule. In certain embodiments, an HNH-like domain is atleast 15, 20, or 25 amino acids in length but not more than 40, 35, or30 amino acids in length, e.g., 20 to 35 amino acids in length, e.g., 25to 30 amino acids in length. Exemplary HNH-like domains are describedbelow.

In an embodiment, a Cas9 molecule or Cas9 polypeptide comprises anHNH-like domain having an amino acid sequence of Formula IX:

(SEQ ID NO: 25) X₁-X₂-X₃-H-X₄-X₅-P-X₆-X₇-X₈-X₉-X₁₀-X₁₁-X₁₂-X₁₃-X₁₄-X₁₅-N-X₁₆-X₁₇-X₁₈-X₁₉-X₂₀-X₂₁-X₂₂-X₂₃-N,

wherein

X₁ is selected from D, E, Q, and N (e.g., D and E);

X² is selected from L, I, R, Q, V, M, and K;

X₃ is selected from D and E;

X₄ is selected from I, V, T, A, and L (e.g., A, I, and V);

X₅ is selected from V, Y, I, L, F, and W (e.g., V, I, and L);

X₆ is selected from Q, H, R, K, Y, I, L, F, and W;

X₇ is selected from S, A, D, T, and K (e.g., S and A);

X₈ is selected from F, L, V, K, Y, M, I, R, A, E, D, and Q (e.g., F);

X₉ is selected from L, R, T, I, V, S, C, Y, K, F, and G;

X₁₀ is selected from K, Q, Y, T, F, L, W, M, A, E, G, and S;

X₁₁ is selected from D, S, N, R, L, and T (e.g., D);

X₁₂ is selected from D, N and S;

X₁₃ is selected from S, A, T, G, and R (e.g., S);

X₁₄ is selected from I, L, F, S, R, Y, Q, W, D, K, and H (e.g., I, L,and F);

X₁₅ is selected from D, S, I, N, E, A, H, F, L, Q, M, G, Y, and V;

X₁₆ is selected from K, L, R, M, T, and F (e.g., L, R, and K);

X₁₇ is selected from V, L, I, A, and T;

X₁₈ is selected from L, I, V, and A (e.g., L and I);

X₁₉ is selected from T, V, C, E, S, and A (e.g., T and V);

X₂₀ is selected from R, F, T, W, E, L, N, C, K, V, S, Q, I, Y, H, and A;

X₂₁ is selected from S, P, R, K, N, A, H, Q, G, and L;

X₂₂ is selected from D, G, T, N, S, K, A, I, E, L, Q, R, and Y; and

X₂₃ is selected from K, V, A, E, Y, I, C, L, S, T, G, K, M, D, and F.

In certain embodiments, a HNH-like domain differs from a sequence of SEQID NO:25 by at least one but not more than, 2, 3, 4, or 5 residues.

In certain embodiments, the HNH-like domain is cleavage competent. Inother embodiments, the HNH-like domain is cleavage incompetent.

In certain embodiments, a Cas9 molecule or Cas9 polypeptide comprises anHNH-like domain comprising an amino acid sequence of Formula X:

(SEQ ID NO: 26) X₁-X₂-X₃-H-X₄-X₅-P-X₆-S-X₈-X₉-X₁₀-D-D-S-X₁₄-X₁₅-N-K-V-L-X₁₉-X₂₀-X₂₁-X₂₂-X₂₃-N,

wherein

X₁ is selected from D and E;

X₂ is selected from L, I, R, Q, V, M, and K;

X₃ is selected from D and E;

X₄ is selected from I, V, T, A, and L (e.g., A, I, and V);

X₅ is selected from V, Y, I, L, F, and W (e.g., V, I, and L);

X₆ is selected from Q, H, R, K, Y, I, L, F, and W;

X₈ is selected from F, L, V, K, Y, M, I, R, A, E, D, and Q (e.g., F);

X₉ is selected from L, R, T, I, V, S, C, Y, K, F, and G;

X₁₀ is selected from K, Q, Y, T, F, L, W, M, A, E, G, and S;

X₁₄ is selected from I, L, F, S, R, Y, Q, W, D, K, and H (e.g., I, L,and F);

X₁₅ is selected from D, S, I, N, E, A, H, F, L, Q, M, G, Y, and V;

X₁₉ is selected from T, V, C, E, S, and A (e.g., T and V);

X₂₀ is selected from R, F, T, W, E, L, N, C, K, V, S, Q, I, Y, H, and A;

X₂₁ is selected from S, P, R, K, N, A, H, Q, G, and L;

X₂₂ is selected from D, G, T, N, S, K, A, I, E, L, Q, R, and Y; and

X₂₃ is selected from K, V, A, E, Y, I, C, L, S, T, G, K, M, D, and F.

In certain embodiment, the HNH-like domain differs from a sequence ofSEQ ID NO:26 by 1, 2, 3, 4, or 5 residues.

In certain embodiments, a Cas9 molecule or Cas9 polypeptide comprises anHNH-like domain comprising an amino acid sequence of Formula XI.

(SEQ ID NO: 27) X₁-V-X₃-H-I-V-P-X₆-S-X₈-X₉-X₁₀-D-D-S-X₁₄-X₁₅-N-K-V-L-T-X₂₀-X₂₁-X₂₂-X₂₃-N,

wherein

X₁ is selected from D and E;

X₃ is selected from D and E;

X₆ is selected from Q, H, R, K, Y, I, L, and W;

X₈ is selected from F, L, V, K, Y, M, I, R, A, E, D, and Q (e.g., F);

X₉ is selected from L, R, T, I, V, S, C, Y, K, F, and G;

X₁₀ is selected from K, Q, Y, T, F, L, W, M, A, E, G, and S;

X₁₄ is selected from I, L, F, S, R, Y, Q, W, D, K, and H (e.g., I, L,and F);

X₁₅ is selected from D, S, I, N, E, A, H, F, L, Q, M, G, Y, and V;

X₂₀ is selected from R, F, T, W, E, L, N, C, K, V, S, Q, I, Y, H, and A;

X₂₁ is selected from S, P, R, K, N, A, H, Q, G, and L;

X₂₂ is selected from D, G, T, N, S, K, A, I, E, L, Q, R, and Y; and

X₂₃ is selected from K, V, A, E, Y, I, C, L, S, T, G, K, M, D, and F.

In certain embodiments, the HNH-like domain differs from a sequence ofSEQ ID NO:27 by 1, 2, 3, 4, or 5 residues.

In certain embodiments, a Cas9 molecule or Cas9 polypeptide comprises anHNH-like domain having an amino acid sequence of Formula XII.

(SEQ ID NO: 28) D-X₂-D-H-I-X₅-P-Q-X₇-F-X₉-X₁₀-D-X₁₂-S-I-D-N-X₁₆-V-L-X₁₉-X₂₀-S-X₂₂-X₂₃-N,

wherein

X₂ is selected from I and V;

X₅ is selected from I and V;

X₇ is selected from A and S;

X₉ is selected from I and L;

X₁₀ is selected from K and T;

X₁₂ is selected from D and N;

X₁₆ is selected from R, K, and L;

X₁₉ is selected from T and V;

X₂₀ is selected from S, and R;

X₂₂ is selected from K, D, and A; and

X₂₃ is selected from E, K, G, and N (e.g., the Cas9 molecule or Cas9polypeptide can comprise an HNH-like domain as described herein).

In an embodiment, the HNH-like domain differs from a sequence of SEQ IDNO:28 by as many as 1 but no more than 2, 3, 4, or 5 residues.

In certain embodiments, a Cas9 molecule or Cas9 polypeptide comprisesthe amino acid sequence of Formula XIII:

(SEQ ID NO: 24) L-Y-Y-L-Q-N-G-X₁′-D-M-Y-X₂′-X₃′-X₄′-X₅′-L-D-I-X₆′-X₇′-L-S-X₈′-Y-Z-N-R-X₉′-K- X₁₀′-D-X₁₁′-V-P,

wherein

X_(1′) is selected from K and R;

X_(2′) is selected from V and T;

X_(3′) is selected from G and D;

X_(4′) is selected from E, Q and D;

X_(5′) is selected from E and D;

X_(6′) is selected from D, N, and H;

X_(7′) is selected from Y, R, and N;

X_(8′) is selected from Q, D, and N;

X_(9′) is selected from G and E;

X_(10′) is selected from S and G;

X_(11′) is selected from D and N; and

Z is an HNH-like domain, e.g., as described above.

In certain embodiments, the Cas9 molecule or Cas9 polypeptide comprisesan amino acid sequence that differs from a sequence of SEQ ID NO:24 byas many as 1 but not more than 2, 3, 4, or 5 residues.

In certain embodiments, the HNH-like domain differs from a sequence ofan HNH-like domain disclosed herein, e.g., in FIGS. 5A-5C, by as many as1 but not more than 2, 3, 4, or 5 residues. In certain embodiments, 1 orboth of the highly conserved residues identified in FIGS. 5A-5C arepresent.

In certain embodiments, the HNH-like domain differs from a sequence ofan HNH-like domain disclosed herein, e.g., in FIGS. 6A-6B, by as many as1 but not more than 2, 3, 4, or 5 residues. In an embodiment, 1, 2, orall 3 of the highly conserved residues identified in FIGS. 6A-6B arepresent.

Cas9 Activities

In certain embodiments, the Cas9 molecule or Cas9 polypeptide is capableof cleaving a target nucleic acid molecule. Typically, wild-type Cas9molecules cleave both strands of a target nucleic acid molecule. Cas9molecules and Cas9 polypeptides can be engineered to alter nucleasecleavage (or other properties), e.g., to provide a Cas9 molecule or Cas9polypeptide which is a nickase, or which lacks the ability to cleavetarget nucleic acid. A Cas9 molecule or Cas9 polypeptide that is capableof cleaving a target nucleic acid molecule is referred to herein as aneaCas9 (an enzymatically active Cas9) molecule or eaCas9 polypeptide.

In certain embodiments, an eaCas9 molecule or eaCas9 polypeptidecomprises one or more of the following enzymatic activities:

(1) nickase activity, i.e., the ability to cleave a single strand, e.g.,the non-complementary strand or the complementary strand, of a nucleicacid molecule;

(2) double stranded nuclease activity, i.e., the ability to cleave bothstrands of a double stranded nucleic acid and create a double strandedbreak, which in an embodiment is the presence of two nickase activities;

(3) endonuclease activity;

(4) exonuclease activity; and

(5) helicase activity, i.e., the ability to unwind the helical structureof a double stranded nucleic acid.

In certain embodiments, an eaCas9 molecule or eaCas9 polypeptide cleavesboth DNA strands and results in a double stranded break. In certainembodiments, an eaCas9 molecule or eaCas9 polypeptide cleaves only onestrand, e.g., the strand to which the gRNA hybridizes to, or the strandcomplementary to the strand the gRNA hybridizes with. In an embodiment,an eaCas9 molecule or eaCas9 polypeptide comprises cleavage activityassociated with an HNH domain. In an embodiment, an eaCas9 molecule oreaCas9 polypeptide comprises cleavage activity associated with a RuvCdomain. In an embodiment, an eaCas9 molecule or eaCas9 polypeptidecomprises cleavage activity associated with an HNH domain and cleavageactivity associated with a RuvC domain. In an embodiment, an eaCas9molecule or eaCas9 polypeptide comprises an active, or cleavagecompetent, HNH domain and an inactive, or cleavage incompetent, RuvCdomain. In an embodiment, an eaCas9 molecule or eaCas9 polypeptidecomprises an inactive, or cleavage incompetent, HNH domain and anactive, or cleavage competent, RuvC domain.

Some Cas9 molecules or Cas9 polypeptides have the ability to interactwith a gRNA molecule, and in conjunction with the gRNA molecule tolocalize to a core target domain, but are incapable of cleaving thetarget nucleic acid or of cleaving at efficient rates. Cas9 moleculeshaving no, or no substantial, cleavage activity are referred to hereinas eiCas9 molecules or eiCas9 polypeptides. For example, an eiCas9molecule or eiCas9 polypeptide can lack cleavage activity or havesubstantially less, e.g., less than 20%, 10%, 5%, 1%, or 0.1% of thecleavage activity of a reference Cas9 molecule or eiCas9 polypeptide, asmeasured by an assay described herein.

Targeting and PAMs

A Cas9 molecule or Cas9 polypeptide can interact with a gRNA moleculeand, in concert with the gRNA molecule, localize to a site whichcomprises a target domain, and in certain embodiments, a PAM sequence.

In certain embodiments, the ability of an eaCas9 molecule or eaCas9polypeptide to interact with and cleave a target nucleic acid is PAMsequence dependent. A PAM sequence is a sequence in the target nucleicacid. In an embodiment, cleavage of the target nucleic acid occursupstream from the PAM sequence. EaCas9 molecules from differentbacterial species can recognize different sequence motifs (e.g., PAMsequences). In an embodiment, an eaCas9 molecule of S. pyogenesrecognizes the sequence motif NGG and directs cleavage of a targetnucleic acid sequence 1 to 10, e.g., 3 to 5, bp upstream from thatsequence (see, e.g., Mali 2013). In an embodiment, an eaCas9 molecule ofS. thermophilus recognizes the sequence motif NGGNG (SEQ ID NO:199)and/or NNAGAAW (W=A or T) (SEQ ID NO:200) and directs cleavage of atarget nucleic acid sequence 1 to 10, e.g., 3 to 5, bp upstream fromthese sequences (see, e.g., Horvath 2010; Deveau 2008). In anembodiment, an eaCas9 molecule of S. mutans recognizes the sequencemotif NGG and/or NAAR (R=A or G) (SEQ ID NO:201) and directs cleavage ofa target nucleic acid sequence 1 to 10, e.g., 3 to 5 bp, upstream fromthis sequence (see, e.g., Deveau 2008). In an embodiment, an eaCas9molecule of S. aureus recognizes the sequence motif NNGRR (R=A or G)(SEQ ID NO:202) and directs cleavage of a target nucleic acid sequence 1to 10, e.g., 3 to 5, bp upstream from that sequence. In an embodiment,an eaCas9 molecule of S. aureus recognizes the sequence motif NNGRRN(R=A or G) (SEQ ID NO:203) and directs cleavage of a target nucleic acidsequence 1 to 10, e.g., 3 to 5, bp upstream from that sequence. In anembodiment, an eaCas9 molecule of S. aureus recognizes the sequencemotif NNGRRT (R=A or G) (SEQ ID NO:204) and directs cleavage of a targetnucleic acid sequence 1 to 10, e.g., 3 to 5, bp upstream from thatsequence. In an embodiment, an eaCas9 molecule of S. aureus recognizesthe sequence motif NNGRRV (R=A or G, V=A, G, or C) (SEQ ID NO:205) anddirects cleavage of a target nucleic acid sequence 1 to 10, e.g., 3 to5, bp upstream from that sequence. The ability of a Cas9 molecule torecognize a PAM sequence can be determined, e.g., using a transformationassay as described previously (Jinek 2012). In each of theaforementioned embodiments (i.e., SEQ ID NOs:199-205), N can be anynucleotide residue, e.g., any of A, G, C, or T.

As is discussed herein, Cas9 molecules can be engineered to alter thePAM specificity of the Cas9 molecule.

Exemplary naturally occurring Cas9 molecules have been describedpreviously (see, e.g., Chylinski 2013). Such Cas9 molecules include Cas9molecules of a cluster 1 bacterial family, cluster 2 bacterial family,cluster 3 bacterial family, cluster 4 bacterial family, cluster 5bacterial family, cluster 6 bacterial family, a cluster 7 bacterialfamily, a cluster 8 bacterial family, a cluster 9 bacterial family, acluster 10 bacterial family, a cluster 11 bacterial family, a cluster 12bacterial family, a cluster 13 bacterial family, a cluster 14 bacterialfamily, a cluster 15 bacterial family, a cluster 16 bacterial family, acluster 17 bacterial family, a cluster 18 bacterial family, a cluster 19bacterial family, a cluster 20 bacterial family, a cluster 21 bacterialfamily, a cluster 22 bacterial family, a cluster 23 bacterial family, acluster 24 bacterial family, a cluster 25 bacterial family, a cluster 26bacterial family, a cluster 27 bacterial family, a cluster 28 bacterialfamily, a cluster 29 bacterial family, a cluster 30 bacterial family, acluster 31 bacterial family, a cluster 32 bacterial family, a cluster 33bacterial family, a cluster 34 bacterial family, a cluster 35 bacterialfamily, a cluster 36 bacterial family, a cluster 37 bacterial family, acluster 38 bacterial family, a cluster 39 bacterial family, a cluster 40bacterial family, a cluster 41 bacterial family, a cluster 42 bacterialfamily, a cluster 43 bacterial family, a cluster 44 bacterial family, acluster 45 bacterial family, a cluster 46 bacterial family, a cluster 47bacterial family, a cluster 48 bacterial family, a cluster 49 bacterialfamily, a cluster 50 bacterial family, a cluster 51 bacterial family, acluster 52 bacterial family, a cluster 53 bacterial family, a cluster 54bacterial family, a cluster 55 bacterial family, a cluster 56 bacterialfamily, a cluster 57 bacterial family, a cluster 58 bacterial family, acluster 59 bacterial family, a cluster 60 bacterial family, a cluster 61bacterial family, a cluster 62 bacterial family, a cluster 63 bacterialfamily, a cluster 64 bacterial family, a cluster 65 bacterial family, acluster 66 bacterial family, a cluster 67 bacterial family, a cluster 68bacterial family, a cluster 69 bacterial family, a cluster 70 bacterialfamily, a cluster 71 bacterial family, a cluster 72 bacterial family, acluster 73 bacterial family, a cluster 74 bacterial family, a cluster 75bacterial family, a cluster 76 bacterial family, a cluster 77 bacterialfamily, or a cluster 78 bacterial family.

Exemplary naturally occurring Cas9 molecules include a Cas9 molecule ofa cluster 1 bacterial family. Examples include a Cas9 molecule of: S.aureus, S. pyogenes (e.g., strains SF370, MGAS10270, MGAS10750,MGAS2096, MGAS315, MGAS5005, MGAS6180, MGAS9429, NZ131, SSI-1), S.thermophilus (e.g., strain LMD-9), S. pseudoporcinus (e.g., strain SPIN20026), S. mutans (e.g., strains UA159, NN2025), S. macacae (e.g.,strain NCTC11558), S. gallolyticus (e.g., strains UCN34, ATCC BAA-2069),S. equines (e.g., strains ATCC 9812, MGCS 124), S. dysdalactiae (e.g.,strain GGS 124), S. bovis (e.g., strain ATCC 700338), S. anginosus(e.g., strain F0211), S. agalactiae (e.g., strains NEM316, A909),Listeria monocytogenes (e.g., strain F6854), Listeria innocua (L.innocua, e.g., strain Clip 11262), Enterococcus italicus (e.g., strainDSM 15952), or Enterococcus faecium (e.g., strain 1,231,408).

In certain embodiments, a Cas9 molecule or Cas9 polypeptide comprises anamino acid sequence:

having 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%homology with;

differs at no more than, 2, 5, 10, 15, 20, 30, or 40% of the amino acidresidues when compared with;

differs by at least 1, 2, 5, 10 or 20 amino acids, but by no more than100, 80, 70, 60, 50, 40, or 30 amino acids from; or

identical to any Cas9 molecule sequence described herein, or to anaturally occurring Cas9 molecule sequence, e.g., a Cas9 molecule from aspecies listed herein (e.g., SEQ ID NOs:1, 2, 4-6, or 12) or describedin Chylinski 2013. In an embodiment, the Cas9 molecule or Cas9polypeptide comprises one or more of the following activities: a nickaseactivity; a double stranded cleavage activity (e.g., an endonucleaseand/or exonuclease activity); a helicase activity; or the ability,together with a gRNA molecule, to localize to a target nucleic acid.

In certain embodiments, a Cas9 molecule or Cas9 polypeptide comprisesany of the amino acid sequence of the consensus sequence of FIGS. 2A-2G,wherein “*” indicates any amino acid found in the corresponding positionin the amino acid sequence of a Cas9 molecule of S. pyogenes, S.thermophilus, S. mutans, or L. innocua, and“-” indicates absent. In anembodiment, a Cas9 molecule or Cas9 polypeptide differs from thesequence of the consensus sequence disclosed in FIGS. 2A-2G by at least1, but no more than 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid residues.In certain embodiments, a Cas9 molecule or Cas9 polypeptide comprisesthe amino acid sequence of SEQ ID NO:2. In other embodiments, a Cas9molecule or Cas9 polypeptide differs from the sequence of SEQ ID NO:2 byat least 1, but no more than 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acidresidues.

A comparison of the sequence of a number of Cas9 molecules indicate thatcertain regions are conserved. These are identified below as:

region 1 (residues 1 to 180, or in the case of region 1′ residues 120 to180)

region 2 (residues 360 to 480);

region 3 (residues 660 to 720);

region 4 (residues 817 to 900); and

region 5 (residues 900 to 960).

In certain embodiments, a Cas9 molecule or Cas9 polypeptide comprisesregions 1-5, together with sufficient additional Cas9 molecule sequenceto provide a biologically active molecule, e.g., a Cas9 molecule havingat least one activity described herein. In certain embodiments, regions1-5 each independently have 50%, 60%, 70%, 80%, 85%, 90%, 95%, 96%, 97%,98%, or 99% homology with the corresponding residues of a Cas9 moleculeor Cas9 polypeptide described herein, e.g., a sequence from FIGS. 2A-2G(SEQ ID NOs:1, 2, 4, 5, 14).

In certain embodiments, a Cas9 molecule or Cas9 polypeptide comprises anamino acid sequence referred to as region 1:

having 50%, 60%, 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% homologywith amino acids 1-180 (the numbering is according to the motif sequencein FIG. 2; 52% of residues in the four Cas9 sequences in FIGS. 2A-2G areconserved) of the amino acid sequence of Cas9 of S. pyogenes (SEQ IDNO:2);

differs by at least 1, 2, 5, 10 or 20 amino acids but by no more than90, 80, 70, 60, 50, 40, or 30 amino acids from amino acids 1-180 of theamino acid sequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans,or Listeria innocua (SEQ ID NOs:2, 4, 1, and 5, respectively); or

is identical to amino acids 1-180 of the amino acid sequence of Cas9 ofS. pyogenes, S. thermophilus, S. mutans, or L. innocua (SEQ ID NOs:2, 4,1, and 5, respectively).

In certain embodiments, a Cas9 molecule or Cas9 polypeptide comprises anamino acid sequence referred to as region 1′:

having 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or99% homology with amino acids 120-180 (55% of residues in the four Cas9sequences in FIG. 2 are conserved) of the amino acid sequence of Cas9 ofS. pyogenes, S. thermophilus, S. mutans, or L. innocua (SEQ ID NOs:2, 4,1, and 5, respectively);

differs by at least 1, 2, or 5 amino acids but by no more than 35, 30,25, 20, or 10 amino acids from amino acids 120-180 of the amino acidsequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans, or L.innocua (SEQ ID NOs:2, 4, 1, and 5, respectively); or

is identical to amino acids 120-180 of the amino acid sequence of Cas9of S. pyogenes, S. thermophilus, S. mutans, or L. innocua (SEQ ID NOs:2,4, 1, and 5, respectively).

In certain embodiments, a Cas9 molecule or Cas9 polypeptide comprises anamino acid sequence referred to as region 2:

having 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%,or 99% homology with amino acids 360-480 (52% of residues in the fourCas9 sequences in FIG. 2 are conserved) of the amino acid sequence ofCas9 of S. pyogenes, S. thermophilus, S. mutans, or L. innocua (SEQ IDNOs:2, 4, 1, and 5, respectively);

differs by at least 1, 2, or 5 amino acids but by no more than 35, 30,25, 20, or 10 amino acids from amino acids 360-480 of the amino acidsequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans, or L.innocua (SEQ ID NOs:2, 4, 1, and 5, respectively); or

is identical to amino acids 360-480 of the amino acid sequence of Cas9of S. pyogenes, S. thermophilus, S. mutans, or L. innocua (SEQ ID NOs:2,4, 1, and 5, respectively).

In certain embodiments, a Cas9 molecule or Cas9 polypeptide comprises anamino acid sequence referred to as region 3:

having %, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%homology with amino acids 660-720 (56% of residues in the four Cas9sequences in FIG. 2 are conserved) of the amino acid sequence of Cas9 ofS. pyogenes, S. thermophilus, S. mutans, or L. innocua (SEQ ID NOs:2, 4,1, and 5, respectively);

differs by at least 1, 2, or 5 amino acids butby no more than 35, 30,25, 20, or 10 amino acids from amino acids 660-720 of the amino acidsequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans, or L.innocua (SEQ ID NOs:2, 4, 1, and 5, respectively); or

is identical to amino acids 660-720 of the amino acid sequence of Cas9of S. pyogenes, S. thermophilus, S. mutans, or L. innocua (SEQ ID NOs:2,4, 1, and 5, respectively).

In certain embodiments, a Cas9 molecule or Cas9 polypeptide comprises anamino acid sequence referred to as region 4:

having 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%,or 99% homology with amino acids 817-900 (55% of residues in the fourCas9 sequences in FIGS. 2A-2G are conserved) of the amino acid sequenceof Cas9 of S. pyogenes, S. thermophilus, S. mutans, or L. innocua (SEQID NOs:2, 4, 1, and 5, respectively); differs by at least 1, 2, or 5amino acids but by no more than 35, 30, 25, 20, or 10 amino acids fromamino acids 817-900 of the amino acid sequence of Cas9 of S. pyogenes,S. thermophilus, S. mutans, or L. innocua (SEQ ID NOs:2, 4, 1, and 5,respectively); or is identical to amino acids 817-900 of the amino acidsequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans, or L.innocua (SEQ ID NOs:2, 4, 1, and 5, respectively).

In certain embodiments, a Cas9 molecule or Cas9 polypeptide comprises anamino acid sequence referred to as region 5:

having 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%,or 99% homology with amino acids 900-960 (60% of residues in the fourCas9 sequences in FIGS. 2A-2G are conserved) of the amino acid sequenceof Cas9 of S. pyogenes, S. thermophilus, S. mutans, or L. innocua (SEQID NOs:2, 4, 1, and 5, respectively);

differs by at least 1, 2, or 5 amino acids but by no more than 35, 30,25, 20, or 10 amino acids from amino acids 900-960 of the amino acidsequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans, or L.innocua (SEQ ID NOs:2, 4, 1, and 5, respectively); or

is identical to amino acids 900-960 of the amino acid sequence of Cas9of S. pyogenes, S. thermophilus, S. mutans, or L. innocua (SEQ ID NOs:2,4, 1, and 5, respectively).

Engineered or Altered Cas9

Cas9 molecules and Cas9 polypeptides described herein can possess any ofa number of properties, including nuclease activity (e.g., endonucleaseand/or exonuclease activity); helicase activity; the ability toassociate functionally with a gRNA molecule; and the ability to target(or localize to) a site on a nucleic acid (e.g., PAM recognition andspecificity). In certain embodiments, a Cas9 molecule or Cas9polypeptide can include all or a subset of these properties. In atypical embodiment, a Cas9 molecule or Cas9 polypeptide has the abilityto interact with a gRNA molecule and, in concert with the gRNA molecule,localize to a site in a nucleic acid. Other activities, e.g., PAMspecificity, cleavage activity, or helicase activity can vary morewidely in Cas9 molecules and Cas9 polypeptides.

Cas9 molecules include engineered Cas9 molecules and engineered Cas9polypeptides (engineered, as used in this context, means merely that theCas9 molecule or Cas9 polypeptide differs from a reference sequences,and implies no process or origin limitation). An engineered Cas9molecule or Cas9 polypeptide can comprise altered enzymatic properties,e.g., altered nuclease activity (as compared with a naturally occurringor other reference Cas9 molecule) or altered helicase activity. Asdiscussed herein, an engineered Cas9 molecule or Cas9 polypeptide canhave nickase activity (as opposed to double strand nuclease activity).In certain embodiments, an engineered Cas9 molecule or Cas9 polypeptidecan have an alteration that alters its size, e.g., a deletion of aminoacid sequence that reduces its size, e.g., without significant effect onone or more Cas9 activities. In certain embodiments, an engineered Cas9molecule or Cas9 polypeptide can comprise an alteration that affects PAMrecognition, e.g., an engineered Cas9 molecule can be altered torecognize a PAM sequence other than that recognized by the endogenouswild-type PI domain. In certain embodiments, a Cas9 molecule or Cas9polypeptide can differ in sequence from a naturally occurring Cas9molecule but not have significant alteration in one or more Cas9activities.

Cas9 molecules or Cas9 polypeptides with desired properties can be madein a number of ways, e.g., by alteration of a parental, e.g., naturallyoccurring, Cas9 molecules or Cas9 polypeptides, to provide an alteredCas9 molecule or Cas9 polypeptide having a desired property. Forexample, one or more mutations or differences relative to a parentalCas9 molecule, e.g., a naturally occurring or engineered Cas9 molecule,can be introduced. Such mutations and differences comprise:substitutions (e.g., conservative substitutions or substitutions ofnon-essential amino acids); insertions; or deletions. In an embodiment,a Cas9 molecule or Cas9 polypeptide can comprises one or more mutationsor differences, e.g., at least 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, or 50mutations but less than 200, 100, or 80 mutations relative to areference, e.g., a parental, Cas9 molecule.

In certain embodiments, a mutation or mutations do not have asubstantial effect on a Cas9 activity, e.g., a Cas9 activity describedherein. In other embodiments, a mutation or mutations have a substantialeffect on a Cas9 activity, e.g., a Cas9 activity described herein.

Non-Cleaving and Modified-Cleavage Cas9

In an embodiment, a Cas9 molecule or Cas9 polypeptide comprises acleavage property that differs from naturally occurring Cas9 molecules,e.g., that differs from the naturally occurring Cas9 molecule having theclosest homology. For example, a Cas9 molecule or Cas9 polypeptide candiffer from naturally occurring Cas9 molecules, e.g., a Cas9 molecule ofS. pyogenes, as follows: its ability to modulate, e.g., decreased orincreased, cleavage of a double stranded nucleic acid (endonucleaseand/or exonuclease activity), e.g., as compared to a naturally occurringCas9 molecule (e.g., a Cas9 molecule of S. pyogenes); its ability tomodulate, e.g., decreased or increased, cleavage of a single strand of anucleic acid, e.g., a non-complementary strand of a nucleic acidmolecule or a complementary strand of a nucleic acid molecule (nickaseactivity), e.g., as compared to a naturally occurring Cas9 molecule(e.g., a Cas9 molecule of S. pyogenes); or the ability to cleave anucleic acid molecule, e.g., a double stranded or single strandednucleic acid molecule, can be eliminated.

In certain embodiments, an eaCas9 molecule or eaCas9 polypeptidecomprises one or more of the following activities: cleavage activityassociated with an N-terminal RuvC-like domain; cleavage activityassociated with an HNH-like domain; cleavage activity associated with anHNH-like domain and cleavage activity associated with an N-terminalRuvC-like domain.

In certain embodiments, an eaCas9 molecule or eaCas9 polypeptidecomprises an active, or cleavage competent, HNH-like domain (e.g., anHNH-like domain described herein, e.g., SEQ ID NOs:24-28) and aninactive, or cleavage incompetent, N-terminal RuvC-like domain. Anexemplary inactive, or cleavage incompetent N-terminal RuvC-like domaincan have a mutation of an aspartic acid in an N-terminal RuvC-likedomain, e.g., an aspartic acid at position 9 of the consensus sequencedisclosed in FIGS. 2A-2G or an aspartic acid at position 10 of SEQ IDNO:2, e.g., can be substituted with an alanine. In an embodiment, theeaCas9 molecule or eaCas9 polypeptide differs from wild-type in theN-terminal RuvC-like domain and does not cleave the target nucleic acid,or cleaves with significantly less efficiency, e.g., less than 20, 10,5, 1, or 0.1% of the cleavage activity of a reference Cas9 molecule,e.g., as measured by an assay described herein. The reference Cas9molecule can by a naturally occurring unmodified Cas9 molecule, e.g., anaturally occurring Cas9 molecule such as a Cas9 molecule of S.pyogenes, or S. thermophilus. In an embodiment, the reference Cas9molecule is the naturally occurring Cas9 molecule having the closestsequence identity or homology.

In an embodiment, an eaCas9 molecule or eaCas9 polypeptide comprises aninactive, or cleavage incompetent, HNH domain and an active, or cleavagecompetent, N-terminal RuvC-like domain (e.g., a RuvC-like domaindescribed herein, e.g., SEQ ID NOs:15-23). Exemplary inactive, orcleavage incompetent HNH-like domains can have a mutation at one or moreof: a histidine in an HNH-like domain, e.g., a histidine shown atposition 856 of the consensus sequence disclosed in FIGS. 2A-2G, e.g.,can be substituted with an alanine; and one or more asparagines in anHNH-like domain, e.g., an asparagine shown at position 870 of theconsensus sequence disclosed in FIGS. 2A-2G and/or at position 879 ofthe consensus sequence disclosed in FIGS. 2A-2G, e.g., can besubstituted with an alanine. In an embodiment, the eaCas9 differs fromwild-type in the HNH-like domain and does not cleave the target nucleicacid, or cleaves with significantly less efficiency, e.g., less than 20,10, 5, 1, or 0.10% of the cleavage activity of a reference Cas9molecule, e.g., as measured by an assay described herein. The referenceCas9 molecule can by a naturally occurring unmodified Cas9 molecule,e.g., a naturally occurring Cas9 molecule such as a Cas9 molecule of S.pyogenes or S. thermophilus. In an embodiment, the reference Cas9molecule is the naturally occurring Cas9 molecule having the closestsequence identity or homology.

In certain embodiments, exemplary Cas9 activities comprise one or moreof PAM specificity, cleavage activity, and helicase activity. Amutation(s) can be present, e.g., in: one or more RuvC domains, e.g., anN-terminal RuvC domain; an HNH domain; a region outside the RuvC domainsand the HNH domain. In an embodiment, a mutation(s) is present in a RuvCdomain. In an embodiment, a mutation(s) is present in an HNH domain. Inan embodiment, mutations are present in both a RuvC domain and an HNHdomain.

Exemplary mutations that may be made in the RuvC domain or HNH domainwith reference to the S. pyogenes sequence include: D10A, E762A, H840A,N854A, N863A, and/or D986A.

In certain embodiments, a Cas9 molecule may be an eiCas9 moleculecomprising one or more differences in a RuvC domain and/or HNH domain ascompared to a reference Cas9 molecule, wherein the eiCas9 molecule doesnot cleave a nucleic acid or cleaves with significantly less efficiencythan the reference Cas9 molecule, e.g., in a cleavage assay as describedherein, e.g., the eiCas9 molecule cuts with 50%, 25%, 10%, or 1% lessefficiency than a reference Cas9 molecule, e.g., the correspondingwild-type Cas9 molecule.

Whether or not a particular sequence, e.g., a substitution, may affectone or more activity, such as targeting activity, cleavage activity,etc., can be evaluated or predicted, e.g., by evaluating whether themutation is conservative. In an embodiment, a “non-essential” amino acidresidue, as used in the context of a Cas9 molecule, is a residue thatcan be altered from the wild-type sequence of a Cas9 molecule, e.g., anaturally occurring Cas9 molecule, e.g., an eaCas9 molecule, withoutabolishing or more preferably, without substantially altering a Cas9activity (e.g., cleavage activity), whereas changing an “essential”amino acid residue results in a substantial loss of activity (e.g.,cleavage activity).

In an embodiment, a Cas9 molecule comprises a cleavage property thatdiffers from naturally occurring Cas9 molecules, e.g., that differs fromthe naturally occurring Cas9 molecule having the closest homology. Forexample, a Cas9 molecule can differ from naturally occurring Cas9molecules, e.g., a Cas9 molecule of S aureus, S. pyogenes, or C. jejunias follows: its ability to modulate, e.g., decreased or increased,cleavage of a double stranded break (endonuclease and/or exonucleaseactivity), e.g., as compared to a naturally occurring Cas9 molecule(e.g., a Cas9 molecule of S aureus, S. pyogenes, or C. jejuni); itsability to modulate, e.g., decreased or increased, cleavage of a singlestrand of a nucleic acid, e.g., a non-complimentary strand of a nucleicacid molecule or a complementary strand of a nucleic acid molecule(nickase activity), e.g., as compared to a naturally occurring Cas9molecule (e.g., a Cas9 molecule of S aureus, S. pyogenes, or C. jejuni);or the ability to cleave a nucleic acid molecule, e.g., a doublestranded or single stranded nucleic acid molecule, can be eliminated.

In an embodiment, the altered Cas9 molecule is an eaCas9 moleculecomprising one or more of the following activities: cleavage activityassociated with a RuvC domain; cleavage activity associated with an HNHdomain; cleavage activity associated with an HNH domain and cleavageactivity associated with a RuvC domain.

In certain embodiments, the altered Cas9 molecule is an eiCas9 moleculewhich does not cleave a nucleic acid molecule (either a double-strandedor single-stranded nucleic acid molecule) or cleaves a nucleic acidmolecule with significantly less efficiency, e.g., less than 20%, 10%,5%, 1%, or 0.1% of the cleavage activity of a reference Cas9 molecule,e.g., as measured by an assay described herein. The reference Cas9molecule can be a naturally occurring unmodified Cas9 molecule, e.g., anaturally occurring Cas9 molecule such as a Cas9 molecule of S.pyogenes, S. thermophilus, S. aureus, C. jejuni or N. meningitidis. Incertain embodiments, the reference Cas9 molecule is the naturallyoccurring Cas9 molecule having the closest sequence identity orhomology. In certain embodiments, the eiCas9 molecule lacks substantialcleavage activity associated with a RuvC domain and/or cleavage activityassociated with an HNH domain.

In certain embodiments, the altered Cas9 molecule or Cas9 polypeptidecomprises a sequence in which:

the sequence corresponding to the fixed sequence of the consensussequence disclosed in FIGS. 2A-2G differs at no more than 1, 2, 3, 4, 5,10, 15, or 20% of the fixed residues in the consensus sequence disclosedin FIGS. 2A-2G; and

the sequence corresponding to the residues identified by “*” in theconsensus sequence disclosed in FIGS. 2A-2G differs at no more than 1,2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40% of the “*” residues from thecorresponding sequence of naturally occurring Cas9 molecule, e.g., an S.thermophilus, S. mutans, S. pyogenes, or L. innocua Cas9 molecule.

In an embodiment, the altered Cas9 molecule or Cas9 polypeptide is aneaCas9 molecule or eaCas9 polypeptide comprising the amino acid sequenceof S. thermophilus Cas9 disclosed in FIGS. 2A-2G (SEQ ID NO:4) with oneor more amino acids that differ from the sequence of S. thermophilus(e.g., substitutions) at one or more residues (e.g., 2, 3, 5, 10, 15,20, 30, 50, 70, 80, 90, 100, or 200 amino acid residues) represented byan “*” in the consensus sequence disclosed in FIGS. 2A-2G (SEQ IDNO:14).

In an embodiment, the altered Cas9 molecule or Cas9 polypeptide is aneaCas9 molecule or eaCas9 polypeptide comprising the amino acid sequenceof S. mutans Cas9 disclosed in FIGS. 2A-2G (SEQ ID NO:1) with one ormore amino acids that differ from the sequence of S. mutans (e.g.,substitutions) at one or more residues (e.g., 2, 3, 5, 10, 15, 20, 30,50, 70, 80, 90, 100, or 200 amino acid residues) represented by an “*”in the consensus sequence disclosed in FIGS. 2A-2G (SEQ ID NO:14).

In an embodiment, the altered Cas9 molecule or Cas9 polypeptide is aneaCas9 molecule or eaCas9 polypeptide comprising the amino acid sequenceof S. pyogenes Cas9 disclosed in FIGS. 2A-2G (SEQ ID NO:2) with one ormore amino acids that differ from the sequence of S. pyogenes (e.g.,substitutions) at one or more residues (e.g., 2, 3, 5, 10, 15, 20, 30,50, 70, 80, 90, 100, or 200 amino acid residues) represented by an “*”in the consensus sequence disclosed in FIGS. 2A-2G (SEQ ID NO:14).

In an embodiment, the altered Cas9 molecule or Cas9 polypeptide is aneaCas9 molecule or eaCas9 polypeptide comprising the amino acid sequenceof L. innocua Cas9 disclosed in FIGS. 2A-2G (SEQ ID NO:5) with one ormore amino acids that differ from the sequence of L. innocua (e.g.,substitutions) at one or more residues (e.g., 2, 3, 5, 10, 15, 20, 30,50, 70, 80, 90, 100, or 200 amino acid residues) represented by an “*”in the consensus sequence disclosed in FIGS. 2A-2G (SEQ ID NO:14).

In certain embodiments, the altered Cas9 molecule or Cas9 polypeptide,e.g., an eaCas9 molecule or eaCas9 polypeptide, can be a fusion, e.g.,of two of more different Cas9 molecules, e.g., of two or more naturallyoccurring Cas9 molecules of different species. For example, a fragmentof a naturally occurring Cas9 molecule of one species can be fused to afragment of a Cas9 molecule of a second species. As an example, afragment of a Cas9 molecule of S. pyogenes comprising an N-terminalRuvC-like domain can be fused to a fragment of Cas9 molecule of aspecies other than S. pyogenes (e.g., S. thermophilus) comprising anHNH-like domain.

Cas9 with Altered or No PAM Recognition

Naturally occurring Cas9 molecules can recognize specific PAM sequences,for example the PAM recognition sequences described above for, e.g., S.pyogenes, S. thermophilus, S. mutans, and S. aureus.

In certain embodiments, a Cas9 molecule or Cas9 polypeptide has the samePAM specificities as a naturally occurring Cas9 molecule. In otherembodiments, a Cas9 molecule or Cas9 polypeptide has a PAM specificitynot associated with a naturally occurring Cas9 molecule, or a PAMspecificity not associated with the naturally occurring Cas9 molecule towhich it has the closest sequence homology. For example, a naturallyoccurring Cas9 molecule can be altered, e.g., to alter PAM recognition,e.g., to alter the PAM sequence that the Cas9 molecule or Cas9polypeptide recognizes in order to decrease off-target sites and/orimprove specificity; or eliminate a PAM recognition requirement. Incertain embodiments, a Cas9 molecule or Cas9 polypeptide can be altered,e.g., to increase length of PAM recognition sequence and/or improve Cas9specificity to high level of identity (e.g., 98%, 99%, or 100% matchbetween gRNA and a PAM sequence), e.g., to decrease off-target sitesand/or increase specificity. In certain embodiments, the length of thePAM recognition sequence is at least 4, 5, 6, 7, 8, 9, 10, or 15 aminoacids in length. In an embodiment, the Cas9 specificity requires atleast 90%, 95%, 96%, 97%, 98%, 99% or more homology between the gRNA andthe PAM sequence. Cas9 molecules or Cas9 polypeptides that recognizedifferent PAM sequences and/or have reduced off-target activity can begenerated using directed evolution. Exemplary methods and systems thatcan be used for directed evolution of Cas9 molecules are described (see,e.g., Esvelt 2011). Candidate Cas9 molecules can be evaluated, e.g., bymethods described herein.

Size-Optimized Cas9

Engineered Cas9 molecules and engineered Cas9 polypeptides describedherein include a Cas9 molecule or Cas9 polypeptide comprising a deletionthat reduces the size of the molecule while still retaining desired Cas9properties, e.g., essentially native conformation, Cas9 nucleaseactivity, and/or target nucleic acid molecule recognition. Providedherein are Cas9 molecules or Cas9 polypeptides comprising one or moredeletions and optionally one or more linkers, wherein a linker isdisposed between the amino acid residues that flank the deletion.Methods for identifying suitable deletions in a reference Cas9 molecule,methods for generating Cas9 molecules with a deletion and a linker, andmethods for using such Cas9 molecules will be apparent to one ofordinary skill in the art upon review of this document.

A Cas9 molecule, e.g., a S. aureus, S. pyogenes, or C. jejuni, Cas9molecule, having a deletion is smaller, e.g., has reduced number ofamino acids, than the corresponding naturally-occurring Cas9 molecule.The smaller size of the Cas9 molecules allows increased flexibility fordelivery methods, and thereby increases utility for genome-editing. ACas9 molecule can comprise one or more deletions that do notsubstantially affect or decrease the activity of the resultant Cas9molecules described herein. Activities that are retained in the Cas9molecules comprising a deletion as described herein include one or moreof the following:

a nickase activity, i.e., the ability to cleave a single strand, e.g.,the non-complementary strand or the complementary strand, of a nucleicacid molecule; a double stranded nuclease activity, i.e., the ability tocleave both strands of a double stranded nucleic acid and create adouble stranded break, which in an embodiment is the presence of twonickase activities;

an endonuclease activity;

an exonuclease activity;

a helicase activity, i.e., the ability to unwind the helical structureof a double stranded nucleic acid;

and recognition activity of a nucleic acid molecule, e.g., a targetnucleic acid or a gRNA.

Activity of the Cas9 molecules described herein can be assessed usingthe activity assays described herein or in the art.

Identifying Regions Suitable for Deletion

Suitable regions of Cas9 molecules for deletion can be identified by avariety of methods. Naturally-occurring orthologous Cas9 molecules fromvarious bacterial species, e.g., any one of those listed in Table 1, canbe modeled onto the crystal structure of S. pyogenes Cas9 (Nishimasu2014) to examine the level of conservation across the selected Cas9orthologs with respect to the three-dimensional conformation of theprotein. Less conserved or unconserved regions that are spatiallylocated distant from regions involved in Cas9 activity, e.g., interfacewith the target nucleic acid molecule and/or gRNA, represent regions ordomains are candidates for deletion without substantially affecting ordecreasing Cas9 activity.

Nucleic Acids Encoding Cas9 Molecules

Nucleic acids encoding the Cas9 molecules or Cas9 polypeptides, e.g., aneaCas9 molecule or eaCas9 polypeptides are provided herein. Exemplarynucleic acids encoding Cas9 molecules or Cas9 polypeptides have beendescribed previously (see, e.g., Cong 2013; Wang 2013; Mali 2013; Jinek2012).

In an embodiment, a nucleic acid encoding a Cas9 molecule or Cas9polypeptide can be a synthetic nucleic acid sequence. For example, thesynthetic nucleic acid molecule can be chemically modified, e.g., asdescribed herein. In an embodiment, the Cas9 mRNA has one or more (e.g.,all of the following properties: it is capped, polyadenylated,substituted with 5-methylcytidine and/or pseudouridine.

In addition, or alternatively, the synthetic nucleic acid sequence canbe codon optimized, e.g., at least one non-common codon or less-commoncodon has been replaced by a common codon. For example, the syntheticnucleic acid can direct the synthesis of an optimized messenger mRNA,e.g., optimized for expression in a mammalian expression system, e.g.,described herein.

In addition, or alternatively, a nucleic acid encoding a Cas9 moleculeor Cas9 polypeptide may comprise a nuclear localization sequence (NLS).Nuclear localization sequences are known in the art.

An exemplary codon optimized nucleic acid sequence encoding a Cas9molecule of S. pyogenes is set forth in SEQ ID NO:3. The correspondingamino acid sequence of an S. pyogenes Cas9 molecule is set forth in SEQID NO:2.

An exemplary codon optimized nucleic acid sequence encoding a Cas9molecule of S. aureus is set forth in SEQ ID NO:7. An amino acidsequence of an S. aureus Cas9 molecule is set forth in SEQ ID NO:6.

Provided below is an exemplary codon optimized nucleic acid sequenceencoding a Cas9 molecule of S. aureus Cas9.

If any of the above Cas9 sequences are fused with a peptide orpolypeptide at the C-terminus, it is understood that the stop codon willbe removed.

Other Cas Molecules and Cas Polypeptides

Various types of Cas molecules or Cas polypeptides can be used topractice the inventions disclosed herein. In some embodiments, Casmolecules of Type II Cas systems are used. In other embodiments, Casmolecules of other Cas systems are used. For example, Type I or Type IIICas molecules may be used. Exemplary Cas molecules (and Cas systems)have been described previously (see, e.g., Haft 2005 and Makarova 2011).Exemplary Cas molecules (and Cas systems) are also shown in Table 2.

Functional Analyses of Candidate Molecules

Candidate Cas9 molecules, candidate gRNA molecules, and candidate Cas9molecule/gRNA molecule complexes can be evaluated by art-knowntechniques or as described herein. Each technique described herein maybe used alone or in combination with one or more techniques to evaluatethe candidate molecule. The techniques disclosed herein may be used fora variety of methods including, without limitation, methods ofdetermining the stability of a Cas9 molecule/gRNA molecule complex,methods of determining a condition that promotes a stable Cas9molecule/gRNA molecule complex, methods of screening for a stable Cas9molecule/gRNA molecule complex, methods of identifying an optimal gRNAto form a stable Cas9 molecule/gRNA molecule complex, methods ofscreening for a Cas9 molecule/gRNA molecule complex for administrationto a subject, and methods of selecting a Cas9 molecule/gRNA moleculecomplex for administration to a subject.

Techniques for Measuring Thermostability of Cas9/gRNA Complexes

The thermostability of Cas9-gRNA ribonucleoprotein (RNP) complexes canbe detected by differential scanning fluorimetry (DSF) and othertechniques. The thermostability of a protein can increase underfavorable conditions such as the addition of a binding RNA molecule,e.g., a gRNA. Thus, information regarding the thermostability of aCas9/gRNA complex is useful for determining whether the complex isstable.

Differential Scanning Fluorimetry (DSF)

DSF is a technique that may be used to measure the thermostability of aprotein. The assay can be applied in a number of ways. Exemplaryprotocols include, but are not limited to, a protocol to determine thedesired solution conditions for RNP formation (assay 1, see below), aprotocol to test the desired stoichiometric ratio of gRNA:Cas9 protein(assay 2, see below), a protocol to screen for effective gRNA moleculesfor Cas9 molecules, e.g., wild-type or mutant Cas9 molecules (assay 3,see below), and a protocol to examine RNP formation in the presence oftarget DNA (assay 4).

Assay 1

To determine the desired solution to form RNP complexes, a 2 μM solutionof Cas9 is made in water with 10× SYPRO Orange® (Life Technologies cat#S-6650) and dispensed into a 384 well plate. An equimolar amount ofgRNA diluted in solutions with varied pH and salt is then added. Afterincubating at room temperature for 10 minutes and centrifugation at 2000rpm to remove any bubbles, a Bio-Rad CFX384™ Real-Time System C1000Touch™ Thermal Cycler with the Bio-Rad CFX Manager software is used torun a gradient from 20° C. to 90° C. with a 1° C. increase intemperature every 10 seconds.

Assay 2

The second assay includes mixing various concentrations of gRNAmolecules with 2 μM Cas9 in the buffer from assay 1 above and incubatingat RT for 10 minutes in a 384 well plate. An equal volume of optimalbuffer with 10× SYPRO Orange® (Life Technologies cat #S-6650) is addedand the plate is sealed with Microseal® B adhesive (MSB-1001). Followingcentrifugation at 2000 rpm to remove any bubbles, a Bio-Rad CFX384™Real-Time System C1000 Touch™ Thermal Cycler with the Bio-Rad CFXManager software is used to run a gradient from 20° C. to 90° C. with a1° C. increase in temperature every 10 seconds.

Assay 3

In the third assay, a Cas9 molecule (e.g., a Cas9 protein, e.g., a Cas9variant protein) of interest is purified. A library of variant gRNAmolecules is synthesized and resuspended to a concentration of 20 μM.The Cas9 molecule is incubated with the gRNA molecule at a finalconcentration of 1 μM each in a predetermined buffer in the presence of5× SYPRO Orange® (Life Technologies cat #S-6650). After incubating atroom temperature for 10 minutes and centrifugation at 2000 rpm for 2minutes to remove any bubbles, a Bio-Rad CFX384™ Real-Time System C1000Touch™ Thermal Cycler with the Bio-Rad CFX Manager software is used torun a gradient from 20° C. to 90° C. with an increase of 1° C. intemperature every 10 seconds.

Assay 4

In the fourth assay, a DSF experiment is performed with the followingsamples: Cas9 protein alone, Cas9 protein with gRNA, Cas9 protein withgRNA and target DNA, and Cas9 protein with target DNA. The order ofmixing components is: reaction solution, Cas9 protein, gRNA, DNA, andSYPRO Orange. The reaction solution contains 10 mM HEPES pH 7.5, 100 mMNaCl, in the absence or presence of MgCl₂. Following centrifugation at2000 rpm for 2 minutes to remove any bubbles, a Bio-Rad CFX384™Real-Time System C1000 Touch™ Thermal Cycler with the Bio-Rad CFXManager software is used to run a gradient from 20° C. to 90° C. with a1° increase in temperature every 10 seconds.

Examples 1 and 2 as described herein disclose exemplary results usingDSF to evaluate and determine the stability of Cas9 molecules andCas9/gRNA complexes. As shown herein, a higher T_(m) value of aCas9/gRNA complex compared to the T_(m) value of the Cas9 molecule inthe absence of the gRNA molecule is indicative of a tighter complexbetween Cas9 and gRNA. Thus, information regarding the T_(m) of Cas9molecules and Cas9/gRNA complexes is useful for determining whether theCas9/gRNA complex is stable.

In addition to DSF, there are a number of additional techniques known inthe art that may be used for determining the stability of the Cas9molecule in a Cas9 molecule/gRNA molecule complex or a preparationthereof. These include alternative methods to DSF that measurethermostability, including but not limited to, differential scanningcalorimetry (DSC) and isothermal titration calorimetry (ITC).

DSC

DSC is a technique that is highly precise in measuring thermostabilityof material in different buffers as well as apo vs. complex. Anadvantage to DSC is that it can also provide differences in enthalpy oftransitions between samples. However, DSC requires significantly largerquantities of material to run than DSF (>50 fold more). DSC is lowerthroughput since it can only run a single sample at a time.

ITC

ITC can measure both the thermostability and kinetic rates ofinteractions of two molecules. The advantage of ITC versus othertechniques is that it provides more precise measurements and kineticinformation. However, it requires lower throughput and larger quantitiesof material.

The thermostability techniques disclosed herein may be used to measurethe thermostability of a molecule (e.g., Cas9 molecule), which canincrease under favorable conditions such as the addition of a bindingRNA molecule. In addition, the thermostability of a molecule mayincrease under favorable conditions such as the presence of a component.In certain embodiments, the component may comprise an additive, a smallmolecule, a stabilizing reagent, buffer, pH, salt concentration,glycerol concentration, or other buffer component.

In certain embodiments, a molecule (e.g., Cas9/gRNA complex) may beselected or determined to be stable if the thermostability value of themolecule is greater than the thermostability value of a referencemolecule or a thermostability reference value. In certain embodiments,the thermostability value being measured is the denaturation temperaturevalue of the molecule. For example, in certain embodiments, a molecule(e.g., Cas9/gRNA complex) may be selected or determined to be stable ifthe denaturation temperature value of the molecule is greater than thedenaturation temperature value of a reference molecule or a denaturationtemperature reference value. In certain embodiments, the thermostabilityvalue being measured is the T_(m) value of the molecule. For example, incertain embodiments, a molecule (e.g., Cas9/gRNA complex) may beselected or determined to be stable if the T_(m) value of the moleculeis greater than the T_(m) value of a reference molecule or a T_(m)reference value. In certain embodiments, the reference molecule may bethe Cas9 molecule in the absence of the gRNA molecule.

In certain embodiments, the molecule being evaluated may be selected ordetermined to be stable if the T_(m) value of the molecule is at least1° C., at least 2° C., at least 3° C., at least 4° C., at least 5° C.,at least 6° C., at least 7° C., at least 8° C., at least 9° C., at least10° C., at least 11° C., at least 12° C., at least 13° C., at least 14°C., at least 15° C., at least 16° C., at least 17° C., at least 18° C.,at least 19° C., at least 20° C., at least 21° C., at least 22° C., atleast 23° C., at least 24° C., at least 25° C., at least 26° C., atleast 27° C., at least 28° C., at least 29° C., at least 30° C., atleast 31° C., at least 32° C., at least 33° C., at least 34° C., atleast 35° C., at least 36° C., at least 37° C., at least 38° C., atleast 39° C., at least 40° C., at least 41° C., at least 42° C., atleast 43° C., at least 44° C., at least 45° C., at least 46° C., atleast 47° C., at least 48° C., at least 49° C., or at least 50° C.greater than the T_(m) value of the reference molecule or T_(m)reference value. For example, the molecule being evaluated may beselected or determined to be stable if the T_(m) value of the moleculeis at least 8° C. greater than the reference molecule or T_(m) referencevalue.

In certain embodiments, the molecule being evaluated may be selected ordetermined to be stable if the T_(m) value of the molecule is about 1°C., about 2° C., about 3° C., about 4° C., about 5° C., about 6° C.,about 7° C., about 8° C., about 9° C., about 10° C., about 11° C., about12° C., about 13° C., about 14° C., about 15° C., about 16° C., about17° C., about 18° C., about 19° C., about 20° C., about 21° C., about22° C., about 23° C., about 24° C., about 25° C., about 26° C., about27° C., about 28° C., about 29° C., about 30° C., about 31° C., about32° C., about 33° C., about 34° C., about 35° C., about 36° C., about37° C., about 38° C., about 39° C., about 40° C., about 41° C., about42° C., about 43° C., about 44° C., about 45° C., about 46° C., about47° C., about 48° C., about 49° C., or about 50° C. greater than theT_(m) value of the reference molecule or T_(m) reference value. Forexample, the molecule being evaluated may be selected or determined tobe stable if the T_(m) value of the molecule is about 8° C. greater thanthe reference molecule or T_(m) reference value.

In certain embodiments, the molecule being evaluated may be selected ordetermined to be stable if the T_(m) value of the molecule is about 1°C. to about 5° C., about 6° C. to about 10° C., about 11° C. to about15° C., about 16° C. to about 20° C., about 21° C. to about 25° C.,about 26° C. to about 30° C., about 31° C. to about 35° C., about 36° C.to about 40° C., about 41° C. to about 45° C., about 46° C. to about 50°C. greater than the T_(m) value of the reference molecule or T_(m)reference value. For example, the molecule being evaluated may beselected or determined to be stable if the T_(m) value of the moleculeis about 6° C. to about 10° C. greater than the reference molecule orT_(m) reference value. In certain embodiments, the molecule beingevaluated may be selected or determined to be stable if the T_(m) valueof the molecule is about 8° C. to about 9° C. greater than the referencemolecule or T_(m) reference value.

Provided herein in certain embodiments, the methods herein may includesteps of detecting a T_(m) value of a Cas9 molecule/gRNA moleculecomplex, determining a delta value between the T_(m) value of the Cas9molecule/gRNA molecule complex and a T_(m) value of a reference moleculeor a T_(m) reference value, and determining the Cas9 molecule/gRNAmolecule complex is stable if the delta value is at least 8° C., and theT_(m) value of the Cas9 molecule/gRNA molecule complex is greater thanthe T_(m) value of the reference molecule or the T_(m) reference value.In certain embodiments, the reference molecule may be the Cas9 moleculeabsent the gRNA molecule.

In certain embodiments, the molecule being evaluated may be selected ordetermined to be stable if a delta value between a T_(m) value of themolecule being evaluated and a T_(m) value of a reference molecule or aT_(m) reference value is at least 1° C., at least 2° C., at least 3° C.,at least 4° C., at least 5° C., at least 6° C., at least 7° C., at least8° C., at least 9° C., at least 10° C., at least 11° C., at least 12°C., at least 13° C., at least 14° C., at least 15° C., at least 16° C.,at least 17° C., at least 18° C., at least 19° C., at least 20° C., atleast 21° C., at least 22° C., at least 23° C., at least 24° C., atleast 25° C., at least 26° C., at least 27° C., at least 28° C., atleast 29° C., at least 30° C., at least 31° C., at least 32° C., atleast 33° C., at least 34° C., at least 35° C., at least 36° C., atleast 37° C., at least 38° C., at least 39° C., at least 40° C., atleast 41° C., at least 42° C., at least 43° C., at least 44° C., atleast 45° C., at least 46° C., at least 47° C., at least 48° C., atleast 49° C., or at least 50° C., and the T_(m) value of the moleculebeing evaluated is greater than the T_(m) value of the referencemolecule or the T_(m) reference value. In certain embodiments, themolecule being evaluated may be a CA9 molecule/gRNA molecule complex andthe reference molecule may be the Cas9 molecule absent the gRNAmolecule.

In certain embodiments, the molecule being evaluated may be selected ordetermined to be stable if a delta value between a T_(m) value of themolecule being evaluated and a T_(m) value of a reference molecule or aT_(m) reference value is about 1° C., about 2° C., about 3° C., about 4°C., about 5° C., about 6° C., about 7° C., about 8° C., about 9° C.,about 10° C., about 11° C., about 12° C., about 13° C., about 14° C.,about 15° C., about 16° C., about 17° C., about 18° C., about 19° C.,about 20° C., about 21° C., about 22° C., about 23° C., about 24° C.,about 25° C., about 26° C., about 27° C., about 28° C., about 29° C.,about 30° C., about 31° C., about 32° C., about 33° C., about 34° C.,about 35° C., about 36° C., about 37° C., about 38° C., about 39° C.,about 40° C., about 41° C., about 42° C., about 43° C., about 44° C.,about 45° C., about 46° C., about 47° C., about 48° C., about 49° C., orabout 50° C., and the T_(m) value of the molecule being evaluated isgreater than the T_(m) value of the reference molecule or the T_(m)reference value. For example, a Cas9 molecule/gRNA molecule complex maybe selected or determined to be stable if the delta value is about 8° C.and the T_(m) value of the Cas9 molecule/gRNA molecule complex isgreater than the T_(m) value of the reference molecule or the T_(m)reference value. In certain embodiments, the reference molecule may bethe Cas9 molecule absent the gRNA molecule.

In certain embodiments, the molecule being evaluated may be selected ordetermined to be stable if a delta value between a T_(m) value of themolecule being evaluated and a T_(m) value of a reference molecule or aT_(m) reference value is about 1° C. to about 5° C., about 6° C. toabout 10° C., about 11° C. to about 15° C., about 16° C. to about 20°C., about 21° C. to about 25° C., about 26° C. to about 30° C., about31° C. to about 35° C., about 36° C. to about 40° C., about 41° C. toabout 45° C., about 46° C. to about 50° C., and the T_(m) value of themolecule being evaluated is greater than the T_(m) value of thereference molecule or the T_(m) reference value. For example, a Cas9molecule/gRNA molecule complex may be selected or determined to bestable if the delta value is about 6° C. to about 10° C. and the T_(m)value of the Cas9 molecule/gRNA molecule complex is greater than theT_(m) value of the reference molecule or the T_(m) reference value. Incertain embodiments, the reference molecule may be the Cas9 moleculeabsent the gRNA molecule.

In certain embodiments, the methods used herein may be used to evaluatea plurality of gRNAs having different lengths complexed with Cas9molecules to determine which Cas9/gRNA complex forms a stable Cas9/gRNAcomplex. These methods may also be used to evaluate differentstoichiometries of Cas9 molecules and gRNA molecules to determine whichCas9/gRNA complex forms a stable Cas9/gRNA complex.

In certain embodiments, a plurality of samples, each sample comprising aCas9/gRNA complex may be generated by combining a Cas9 molecule and oneof a plurality of gRNA molecules. In certain embodiments, a T_(m) valueof the Cas9/gRNA complex may be detected in each of the plurality ofsamples. In certain embodiments, at least one sample may be selectedfrom the plurality of samples based on one or more of (i) a comparisonof the T_(m) values in the plurality of samples to a T_(m) value of areference Cas9/gRNA complex or a pre-determined threshold T_(m) value,or (ii) a relative ordering of the T_(m) values of the plurality ofsamples. In certain embodiments, the T_(m) value may be detected by DSF.In certain embodiments, the at least one sample may be selected if theT_(m) value of the Cas9 molecule/gRNA molecule complex is at least 8° C.greater than the T_(m) value of the Cas9 molecule absent the gRNAmolecule.

Techniques for Measuring the Activity of Cas9 and Cas9/gRNA Complexes

In addition to thermostability techniques, there are a variety of othertechniques known in the art that may be used with the methods herein.For example, certain activities of a Cas9 molecule/gRNA molecule complexor molecules thereof can be measured to select or determine whether theCas9 molecule/gRNA molecule complex or molecules thereof are stable.These techniques may be used alone or in conjunction with thethermostability techniques described herein to determine whether a Cas9molecule/gRNA molecule complex or molecules thereof are stable. Thetechniques disclosed herein may be used to detect an activity of themolecule being evaluated (e.g., Cas9 molecule in a Cas9 molecule/gRNAmolecule complex, gRNA molecule in a Cas9 molecule/gRNA moleculecomplex, or Cas9 molecule/gRNA molecule complex or preparation thereof).In certain embodiments, an activity value of the molecule beingevaluated may be measured. In certain embodiments, the molecule beingevaluated may be selected or determined to be stable if the activityvalue of the molecule being evaluated is greater than the activity valueof a reference molecule or an activity reference value.

The various activities of the molecule to be evaluated that may bedetected include the binding activity and cleavage activity of themolecule. The binding activity and cleavage activity of the molecule tobe evaluated may be detected using the techniques described herein.

Some examples of a binding activity of a molecule include, withoutlimitation, the ability of a gRNA molecule to remain hybridized to theDNA target, the ability of a gRNA molecule to bind to the Cas9 moleculeof the Cas9 molecule/gRNA molecule complex, or the ability of a gRNAmolecule to bind to the Cas9 molecule of the Cas9 molecule/gRNA moleculecomplex. In certain embodiments, when a binding activity of a moleculeis being detected, a binding value may be measured. In certainembodiments, the molecule being evaluated may be selected or determinedto be stable if the binding value of the molecule being evaluated isgreater than the binding value of a reference molecule or a bindingreference value.

Some examples of a cleavage activity may include, without limitation,the ability to induce indels, the ability to modify a target DNA, and apropensity of a preselected repair method. In certain embodiments, whenthe cleavage activity is being detected, a cleavage value may bemeasured. In certain embodiments, the molecule being evaluated may beselected or determined to be stable if the cleavage value of themolecule being evaluated is greater than the cleavage value of areference molecule or a cleavage reference value.

Techniques for Measuring the Binding Activity (Kinetics) of Cas9 andCas9 gRNA Complexes

The binding activity of the molecule being evaluated (e.g., Cas9molecule in a Cas9 molecule/gRNA molecule complex, gRNA molecule in aCas9 molecule/gRNA molecule complex, or Cas9 molecule/gRNA moleculecomplex or preparation thereof) can be detected using varioustechniques. The kinetics of binding between two molecules may be morefavorable under certain conditions, such as the presence of a component.In certain embodiments, the component may comprise an additive, a smallmolecule, a stabilizing reagent, buffer, pH, salt concentration,glycerol concentration, or other buffer component. or the addition of aparticular component.

Methods that include detecting the binding activity of Cas9/gRNAcomplexes include, without limitation, detecting the ability of the gRNAmolecule to bind to the Cas9 molecule of the Cas9 molecule/gRNA moleculecomplex and detecting the ability of Cas9 molecules and Cas9/gRNAcomplexes to bind to target DNA. These methods may be performed usingtechniques such as kinetics assays that provide biophysical informationabout the binding of the molecules being evaluated. Some examples ofkinetics assays that may be used are, without limitation, surfaceplasmon resonance (SPR), BioLayer Interferometry (BLI), and gel bandshift assay as described below.

SPR

SPR requires the use of either a BiaCore or ProteOn XPR system. In thistechnique, one molecule is attached either covalently or via an affinitymethod to the surface of a chip. The second molecule is injected into aflow cell and is pushed through via buffer. Changes in the angle ofreflected light lead to changes in the amount of plasmon resonance. Fromthis, kinetic association and disassociation can be measured.

BLI

BLI requires an instrument called the Octet by fortéBio. Similar to SPR,BLI is capable of determining kinetic rates of interaction between twomolecules.

Gel Band Shift Assay

Gel band shift assay (e.g., electrophoretic mobility shift assay) isanother method to determine the K_(D) of two interacting molecules. Thisdetermination is more crude than other available techniques, but has theadvantage that it can be performed with relatively inexpensive reagents.

Binding Assay: Testing the Binding of Cas9 Molecules and Cas9/gRNAComplexes to Target DNA

Exemplary methods for evaluating the binding of Cas9 molecule to targetDNA have been described previously (Jinek 2012). The techniquesdescribed herein, such as SPR, BLI and gel band shift assays may be usedto measure, for example, the ability of a gRNA molecule to bind to theCas9 molecule of the Cas9 molecule/gRNA molecule complex or the abilityof Cas9 molecules and Cas9/gRNA complexes to bind to target DNA.

For example, in an electrophoretic mobility shift assay, target DNAduplexes are formed by mixing of each strand (10 nmol) in deionizedwater, heating to 95° C. for 3 minutes, and slow cooling to roomtemperature. All DNAs are purified on 8% native gels containing 1×TBE.DNA bands are visualized by UV shadowing, excised, and eluted by soakinggel pieces in DEPC-treated H₂O. Eluted DNA is ethanol precipitated anddissolved in DEPC-treated H₂O. DNA samples are 5′ end labeled with[γ-³²P]-ATP using T4 polynucleotide kinase for 30 minutes at 37° C.Polynucleotide kinase is heat denatured at 65° C. for 20 minutes, andunincorporated radiolabel is removed using a column. Binding assays areperformed in buffer containing 20 mM HEPES pH 7.5, 100 mM KCl, 5 mMMgCl₂, 1 mM DTT, and 10% glycerol in a total volume of 10 μL. Cas9protein molecules are programmed with equimolar amounts of pre-annealedgRNA molecule and titrated from 100 μM to 1 μM. Radiolabeled DNA isadded to a final concentration of 20 μM. Samples are incubated for 1hour at 37° C. and resolved at 4° C. on an 8% native polyacrylamide gelcontaining 1×TBE and 5 mM MgCl₂. Gels are dried and DNA visualized byphosphorimaging.

Techniques for Measuring Cleavage Activity of Cas9 gRNA Complexes

Methods described herein may include detecting the cleavage activity ofthe Cas9/gRNA complex. This may include detecting the ability of theCas9/gRNA complex to modify a target DNA, for example, the ability ofthe Cas9/gRNA complex to cleave a target nucleic acid. Some examples oftechniques that may be used to detect the cleavage activity of Cas9/gRNAcomplexes are described herein.

Cleavage Assay: Testing the Endonuclease Activity of Cas9 Molecule/gRNAMolecule Complexes

Additional activities that can be tested to determine the stability of aCas9/gRNA complex include the ability of the Cas9/gRNA complex to modifya target DNA, for example, the ability of the Cas9/gRNA complex tocleave a target nucleic acid. The endonuclease activity of a Cas9/gRNAcomplex may be measured as disclosed herein. For example, exemplarymethods for evaluating the endonuclease activity of Cas9 molecule havebeen described previously (Jinek 2012).

The ability of a Cas9 molecule/gRNA molecule complex to bind to andcleave a target nucleic acid can be evaluated in a plasmid cleavageassay. In this assay, a synthetic or in vitro-transcribed gRNA moleculeis pre-annealed prior to the reaction by heating to 95° C. and slowlycooling down to room temperature. Native or restrictiondigest-linearized plasmid DNA (300 ng (˜8 nM)) is incubated for 60minutes at 37° C. with purified Cas9 protein molecule (50-500 nM) andgRNA (50-500 nM, 1:1) in a Cas9 plasmid cleavage buffer (20 mM HEPES pH7.5, 150 mM KCl, 0.5 mM DTT, 0.1 mM EDTA) with or without 10 mM MgCl₂.The reactions are stopped with 5×DNA loading buffer (30% glycerol, 1.2%SDS, 250 mM EDTA), resolved by a 0.8 or 1% agarose gel electrophoresisand visualized by ethidium bromide staining. The resulting cleavageproducts indicate whether the Cas9 molecule cleaves both DNA strands, oronly one of the two strands. For example, linear DNA products indicatethe cleavage of both DNA strands, while nicked open circular productsindicate that only one of the two strands is cleaved.

Alternatively, the ability of a Cas9 molecule/gRNA molecule complex tobind to and cleave a target nucleic acid can be evaluated in anoligonucleotide DNA cleavage assay. In this assay, DNA oligonucleotides(10 pmol) are radiolabeled by incubating with 5 units T4 polynucleotidekinase and ˜3-6 pmol (˜20-40 mCi) [γ-³²P]-ATP in 1×T4 polynucleotidekinase reaction buffer at 37° C. for 30 minutes, in a 50 μL reaction.After heat inactivation (65° C. for 20 min), reactions are purifiedthrough a column to remove unincorporated label. Duplex substrates (100nM) are generated by annealing labeled oligonucleotides with equimolaramounts of unlabeled complementary oligonucleotide at 95° C. for 3minutes, followed by slow cooling to room temperature. For cleavageassays, gRNA molecules are annealed by heating to 95° C. for 30 seconds,followed by slow cooling to room temperature. Cas9 (500 nM finalconcentration) is pre-incubated with the annealed gRNA molecules (500nM) in cleavage assay buffer (20 mM HEPES pH 7.5, 100 mM KCl, 5 mMMgCl2, 1 mM DTT, 5% glycerol) in a total volume of 9 μL. Reactions areinitiated by the addition of 1 μL target DNA (10 nM) and incubated for 1hour at 37° C. Reactions are quenched by the addition of 20 μL ofloading dye (5 mM EDTA, 0.025% SDS, 5% glycerol in formamide) and heatedto 95° C. for 5 minutes. Cleavage products are resolved on 12%denaturing polyacrylamide gels containing 7 M urea and visualized byphosphorimaging. The resulting cleavage products indicate that whetherthe complementary strand, the non-complementary strand, or both arecleaved.

One or both of these assays can be used to determine the stability of aCas9/gRNA complex and evaluate the suitability of a candidate gRNAmolecule or candidate Cas9 molecule.

Genome Editing Approaches

The methods described herein can be used for evaluating Cas9molecule/gRNA molecule complexes. These Cas9 molecule/gRNA moleculecomplexes can be used to target genes using one or more of theapproaches or pathways discussed herein. In certain embodiments, amutation in a target gene is corrected by HDR using an exogenouslyprovided template nucleic acid. In other embodiments, a mutation in atarget gene is corrected by HDR without using an exogenously providedtemplate nucleic acid. In certain embodiments, one or both alleles of atarget gene are knocked out using NHEJ. In certain embodiments,expression of a target gene is knocked down. The methods describedherein can be used to evaluate whether a Cas9 molecule/gRNA moleculecomplex is desirable for one or more of the approaches or pathwaysdiscussed herein.

HDR Repair and Template Nucleic Acids

As described herein, nuclease-induced HDR can be used to alter a targetposition within a target sequence (e.g., correct, e.g., repair or edit,a mutation in the genome).

In certain embodiments, HDR-based methods for altering a target positionutilize an exogenously provided template nucleic acid (also referred toherein as a donor construct or donor template). While not wishing to bebound by theory, it is believed that alteration of the target positionoccurs by HDR with the exogenously provided donor template or templatenucleic acid. It is contemplated that a plasmid donor template can beused as a template for homologous recombination. It is furthercontemplated that a single stranded donor template can be used as atemplate for alteration of a target position by alternate methods of HDR(e.g., single strand annealing) between the target sequence and thedonor template. Donor template-effected alteration of a target positiondepends on cleavage by a Cas9 molecule. Cleavage by Cas9 can comprise adouble-strand break or two single-strand breaks.

In other embodiments, HDR-based methods for altering a target positiondo not utilize an exogenously provided template nucleic acid. While notwishing to be bound by theory, it is believed that alteration of thetarget position occurs by HDR with an endogenous genomic donor sequence.In certain embodiments, the endogenous genomic donor sequence is locatedon the same chromosome as the target position. In other embodiments, theendogenous genomic donor sequence is located on a different chromosomefrom the target sequence. Alteration of a target position by anendogenous genomic donor sequence depends on cleavage by a Cas9molecule. Cleavage by Cas9 can comprise a double-strand break or twosingle-strand breaks.

Mutations that can be corrected by HDR using a template nucleic acid, orusing endogenous genomic donor sequence, include point mutations. Incertain embodiments, a point mutation can be corrected using either onedouble-strand break or two single-strand breaks. In certain embodiments,a point mutation can be corrected by (1) one double-strand break, (2)two single-strand breaks, (3) two double-strand breaks with a breakoccurring on each side of the target position, (4) one double-strandbreak and two single-strand breaks with the double-strand break and twosingle-strand breaks occurring on each side of the target position, (5)four single-strand breaks with a pair of single-strand breaks occurringon each side of the target position, or (6) one single-strand break.

In certain embodiments wherein a single-stranded template nucleic acidis used, the target position can be altered by alternative HDR.

Donor template-effected alteration of a target position depends oncleavage by a Cas9 molecule. Cleavage by Cas9 can comprise a nick, adouble-strand break, or two single-strand breaks, e.g., one on eachstrand of the target nucleic acid. After introduction of the breaks onthe target nucleic acid, resection occurs at the break ends resulting insingle stranded overhanging DNA regions.

In canonical HDR, a double-stranded donor template is introduced,comprising homologous sequence to the target nucleic acid that willeither be directly incorporated into the target nucleic acid or used asa template to correct the sequence of the target nucleic acid. Afterresection at the break, repair can progress by different pathways, e.g.,by the double Holliday junction model (or double strand break repair,DSBR, pathway) or the synthesis-dependent strand annealing (SDSA)pathway. In the double Holliday junction model, strand invasion by thetwo single stranded overhangs of the target nucleic acid to thehomologous sequences in the donor template occurs, resulting in theformation of an intermediate with two Holliday junctions. The junctionsmigrate as new DNA is synthesized from the ends of the invading strandto fill the gap resulting from the resection. The end of the newlysynthesized DNA is ligated to the resected end, and the junctions areresolved, resulting in the correction of the target nucleic acid, e.g.,incorporation of the correct sequence of the donor template at thecorresponding target position. Crossover with the donor template mayoccur upon resolution of the junctions. In the SDSA pathway, only onesingle stranded overhang invades the donor template and new DNA issynthesized from the end of the invading strand to fill the gapresulting from resection. The newly synthesized DNA then anneals to theremaining single stranded overhang, new DNA is synthesized to fill inthe gap, and the strands are ligated to produce the corrected DNAduplex.

In alternative HDR, a single strand donor template, e.g., templatenucleic acid, is introduced. A nick, single-strand break, ordouble-strand break at the target nucleic acid, for altering a desiredA1AT target position, is mediated by a Cas9 molecule, e.g., describedherein, and resection at the break occurs to reveal single strandedoverhangs. Incorporation of the sequence of the template nucleic acid tocorrect or alter the target position of the target nucleic acidtypically occurs by the SDSA pathway, as described above.

Additional details on template nucleic acids are provided in Section IVentitled “Template nucleic acids” in International ApplicationPCT/US2014/057905.

NHEJ Approaches for Gene Targeting

As described herein, nuclease-induced NHEJ can be used to targetgene-specific knockouts and remove (e.g., delete) sequences in a gene ofinterest.

While not wishing to be bound by theory, it is believed that, in certainembodiments, the genomic alterations associated with the methodsdescribed herein rely on nuclease-induced NHEJ and the error-pronenature of the NHEJ repair pathway. NHEJ repairs a double-strand break inthe DNA by joining together the two ends; however, generally, theoriginal sequence is restored only if two compatible ends, exactly asthey were formed by the double-strand break, are perfectly ligated. TheDNA ends of the double-strand break are frequently the subject ofenzymatic processing, resulting in the addition or removal ofnucleotides, at one or both strands, prior to rejoining of the ends.This results in the presence of insertion and/or deletion (indel)mutations in the DNA sequence at the site of the NHEJ repair. Two-thirdsof these mutations typically alter the reading frame and, therefore,produce a non-functional protein. Additionally, mutations that maintainthe reading frame, but which insert or delete a significant amount ofsequence, can destroy functionality of the protein. This is locusdependent as mutations in critical functional domains are likely lesstolerable than mutations in non-critical regions of the protein.

The indel mutations generated by NHEJ are unpredictable in nature;however, at a given break site certain indel sequences are favored andare over represented in the population, likely due to small regions ofmicrohomology. The lengths of deletions can vary widely; they are mostcommonly in the 1-50 bp range, but can reach greater than 100-200 bp.Insertions tend to be shorter and often include short duplications ofthe sequence immediately surrounding the break site. However, it ispossible to obtain large insertions, and in these cases, the insertedsequence has often been traced to other regions of the genome or toplasmid DNA present in the cells.

Because NHEJ is a mutagenic process, it can also be used to delete smallsequence motifs (e.g., motifs less than or equal to 50 nucleotides inlength) as long as the generation of a specific final sequence is notrequired. If a double-strand break is targeted near to a targetsequence, the deletion mutations caused by the NHEJ repair often span,and therefore remove, the unwanted nucleotides. For the deletion oflarger DNA segments, introducing two double-strand breaks, one on eachside of the sequence, can result in NHEJ between the ends with removalof the entire intervening sequence. In this way, DNA segments as largeas several hundred kilobases can be deleted. Both of these approachescan be used to delete specific DNA sequences; however, the error-pronenature of NHEJ may still produce indel mutations at the site of repair.

Both double strand cleaving eaCas9 molecules and single strand, ornickase, eaCas9 molecules can be used in the methods and compositionsdescribed herein to generate NHEJ-mediated indels. NHEJ-mediated indelstargeted to the gene, e.g., a coding region, e.g., an early codingregion of a gene, of interest can be used to knockout (i.e., eliminateexpression of) a gene of interest. For example, early coding region of agene of interest includes sequence immediately following a start codon,within a first exon of the coding sequence, or within 500 bp of thestart codon (e.g., less than 500, 450, 400, 350, 300, 250, 200, 150,100, or 50 bp).

Targeted Knockdown

Unlike CRISPR/Cas-mediated gene knockout, which permanently eliminatesexpression by mutating the gene at the DNA level, CRISPR/Cas knockdownallows for temporary reduction of gene expression through the use ofartificial transcription factors. Mutating key residues in both DNAcleavage domains of the Cas9 protein (e.g., the D10A and H840Amutations) results in the generation of an enzymatically inactive Cas9(eiCas9, also known as dead Cas9 or dCas9) molecule. An eiCas9 moleculecomplexes with a gRNA and localizes to the DNA sequence specified bythat gRNA's targeting domain, but does cleave the target DNA. Fusion ofeiCas9 to an effector domain, e.g., a transcription repression domain,enables recruitment of the effector to any DNA site specified by thegRNA. Although the eiCas9 molecule itself can block transcription whenrecruited to early regions in the coding sequence, more robustrepression can be achieved by fusing a transcriptional repression domain(e.g., KRAB, SID, or ERD) to the eiCas9 and recruiting it to the targetknockdown position, e.g., within 1000 bp of sequence 3′ to the startcodon or within 500 bp of a promoter region 5′ to a gene start codon. Itis likely that targeting DNAse I hypersensitive sites (DHSs) of thepromoter may yield more efficient gene repression or activation becausethese regions are more likely to be accessible to the Cas9 protein andare also more likely to harbor sites for endogenous transcriptionfactors. Especially for gene repression, it is contemplated herein thatblocking the binding site of an endogenous transcription factor wouldaid in downregulating gene expression. In certain embodiments, one ormore eiCas9 molecules may be used to block binding of one or moreendogenous transcription factors. In other embodiments, an eiCas9molecule can be fused to a chromatin modifying protein. Alteringchromatin status can result in decreased expression of the target gene.One or more eiCas9 molecules fused to one or more chromatin modifyingproteins may be used to alter chromatin status.

In certain embodiments, a gRNA molecule can be targeted to a knowntranscription response element (e.g., promoter, enhancer, etc.), a knownupstream activating sequence (UAS), and/or a sequence of unknown orknown function suspected of being able to control expression of thetarget DNA.

CRISPR/Cas-mediated gene knockdown can be used to reduce expression ofan unwanted allele or transcript. Contemplated herein are scenarioswherein permanent destruction of the gene is not ideal. In thesescenarios, site-specific repression may be used to temporarily reduce oreliminate expression. It is also contemplated herein that the off-targeteffects of a Cas-repressor may be less severe than those of aCas-nuclease as a nuclease can cleave any DNA sequence and causemutations whereas a Cas-repressor may only have an effect if it targetsthe promoter region of an actively transcribed gene. However, whilenuclease-mediated knockout is permanent, repression may only persist aslong as the Cas-repressor is present in the cells. Once the repressor isno longer present, it is likely that endogenous transcription factorsand gene regulatory elements would restore expression to its naturalstate.

Single-Strand Annealing

Single strand annealing (SSA) is another DNA repair process that repairsa double-strand break between two repeat sequences present in a targetnucleic acid. Repeat sequences utilized by the SSA pathway are generallygreater than 30 nucleotides in length. Resection at the break endsoccurs to reveal repeat sequences on both strands of the target nucleicacid. After resection, single strand overhangs containing the repeatsequences are coated with RPA protein to prevent the repeats sequencesfrom inappropriate annealing, e.g., to themselves. RAD52 binds to andeach of the repeat sequences on the overhangs and aligns the sequencesto enable the annealing of the complementary repeat sequences. Afterannealing, the single-strand flaps of the overhangs are cleaved. New DNAsynthesis fills in any gaps, and ligation restores the DNA duplex. As aresult of the processing, the DNA sequence between the two repeats isdeleted. The length of the deletion can depend on many factors includingthe location of the two repeats utilized, and the pathway orprocessivity of the resection.

In contrast to HDR pathways, SSA does not require a template nucleicacid to alter or correct a target nucleic acid sequence. Instead, thecomplementary repeat sequence is utilized.

Other DNA Repair Pathways SSBR (Single Strand Break Repair)

Single-stranded breaks (SSB) in the genome are repaired by the SSBRpathway, which is a distinct mechanism from the DSB repair mechanismsdiscussed above. The SSBR pathway has four major stages: SSB detection,DNA end processing, DNA gap filling, and DNA ligation. A more detailedexplanation is given in Caldecott 2008, and a summary is given here.

In the first stage, when a SSB forms, PARP1 and/or PARP2 recognize thebreak and recruit repair machinery. The binding and activity of PARP1 atDNA breaks is transient and it seems to accelerate SSBR by promoting thefocal accumulation or stability of SSBR protein complexes at the lesion.Arguably the most important of these SSBR proteins is XRCC1, whichfunctions as a molecular scaffold that interacts with, stabilizes, andstimulates multiple enzymatic components of the SSBR process includingthe protein responsible for cleaning the DNA 3′ and 5′ ends. Forinstance, XRCC1 interacts with several proteins (DNA polymerase beta,PNK, and three nucleases, APE1, APTX, and APLF) that promote endprocessing. APE1 has endonuclease activity. APLF exhibits endonucleaseand 3′ to 5′ exonuclease activities. APTX has endonuclease and 3′ to 5′exonuclease activity.

This end processing is an important stage of SSBR since the 3′- and/or5′-termini of most, if not all, SSBs are ‘damaged.’ End processinggenerally involves restoring a damaged 3′-end to a hydroxylated stateand and/or a damaged 5′ end to a phosphate moiety, so that the endsbecome ligation-competent. Enzymes that can process damaged 3′ terminiinclude PNKP, APE1, and TDP1. Enzymes that can process damaged 5′termini include PNKP, DNA polymerase beta, and APTX. LIG3 (DNA ligaseIII) can also participate in end processing. Once the ends are cleaned,gap filling can occur.

At the DNA gap filling stage, the proteins typically present are PARP1,DNA polymerase beta, XRCC1, FEN1 (flap endonuclease 1), DNA polymerasedelta/epsilon, PCNA, and LIG1. There are two ways of gap filling, theshort patch repair and the long patch repair. Short patch repairinvolves the insertion of a single nucleotide that is missing. At someSSBs, “gap filling” might continue displacing two or more nucleotides(displacement of up to 12 bases have been reported). FEN1 is anendonuclease that removes the displaced 5′-residues. Multiple DNApolymerases, including Polo, are involved in the repair of SSBs, withthe choice of DNA polymerase influenced by the source and type of SSB.

In the fourth stage, a DNA ligase such as LIG1 (Ligase I) or LIG3(Ligase III) catalyzes joining of the ends. Short patch repair usesLigase III and long patch repair uses Ligase I.

Sometimes, SSBR is replication-coupled. This pathway can involve one ormore of CtTP, MRN, ERCC1, and FEN1. Additional factors that may promoteSSBR include: aPARP, PARP1, PARP2, PARG, XRCC1, DNA polymerase b, DNApolymerase d, DNA polymerase e, PCNA, LIG1, PNK, PNKP, APE1, APTX, APLF,TDP1, LIG3, FEN1, CtIP, MRN, and ERCC1.

MMR (Mismatch Repair)

Cells contain three excision repair pathways: MMR, BER, and NER. Theexcision repair pathways have a common feature in that they typicallyrecognize a lesion on one strand of the DNA, then exo/endonucleasesremove the lesion and leave a 1-30 nucleotide gap that issub-sequentially filled in by DNA polymerase and finally sealed withligase. A more complete picture is given in Li 2008, and a summary isprovided here.

Mismatch repair (MMR) operates on mispaired DNA bases.

The MSH2/6 or MSH2/3 complexes both have ATPases activity that plays animportant role in mismatch recognition and the initiation of repair.MSH2/6 preferentially recognizes base-base mismatches and identifiesmispairs of 1 or 2 nucleotides, while MSH2/3 preferentially recognizeslarger ID mispairs.

hMLH1 heterodimerizes with hPMS2 to form hMutLα which possesses anATPase activity and is important for multiple steps of MMR. It possessesa PCNA/replication factor C (RFC)-dependent endonuclease activity whichplays an important role in 3′ nick-directed MMR involving EXO1 (EXO1 isa participant in both HR and MMR.) It regulates termination ofmismatch-provoked excision. Ligase I is the relevant ligase for thispathway. Additional factors that may promote MMR include: EXO1, MSH2,MSH3, MSH6, MLH1, PMS2, MLH3, DNA Pol d, RPA, HMGB1, RFC, and DNA ligaseI.

Base Excision Repair (BER)

The base excision repair (BER) pathway is active throughout the cellcycle; it is responsible primarily for removing small,non-helix-distorting base lesions from the genome. In contrast, therelated Nucleotide Excision Repair pathway (discussed in the nextsection) repairs bulky helix-distorting lesions. A more detailedexplanation is given in Caldecott 2008, and a summary is given here.

Upon DNA base damage, base excision repair (BER) is initiated and theprocess can be simplified into five major steps: (a) removal of thedamaged DNA base; (b) incision of the subsequent a basic site; (c)clean-up of the DNA ends; (d) insertion of the correct nucleotide intothe repair gap; and (e) ligation of the remaining nick in the DNAbackbone. These last steps are similar to the SSBR.

In the first step, a damage-specific DNA glycosylase excises the damagedbase through cleavage of the N-glycosidic bond linking the base to thesugar phosphate backbone. Then AP endonuclease-1 (APE1) or bifunctionalDNA glycosylases with an associated lyase activity incised thephosphodiester backbone to create a DNA single strand break (SSB). Thethird step of BER involves cleaning-up of the DNA ends. The fourth stepin BER is conducted by Polo that adds a new complementary nucleotideinto the repair gap and in the final step XRCC1/Ligase III seals theremaining nick in the DNA backbone. This completes the short-patch BERpathway in which the majority (˜80%) of damaged DNA bases are repaired.However, if the 5′-ends in step 3 are resistant to end processingactivity, following one nucleotide insertion by Pol β there is then apolymerase switch to the replicative DNA polymerases, Pol δ/ε, whichthen add ˜2-8 more nucleotides into the DNA repair gap. This creates a5′ flap structure, which is recognized and excised by flapendonuclease-1 (FEN-1) in association with the processivity factorproliferating cell nuclear antigen (PCNA). DNA ligase I then seals theremaining nick in the DNA backbone and completes long-patch BER.Additional factors that may promote the BER pathway include: DNAglycosylase, APE1, Polb, Pold, Pole, XRCC1, Ligase III, FEN-1, PCNA,RECQL4, WRN, MYH, PNKP, and APTX.

Nucleotide Excision Repair (NER)

Nucleotide excision repair (NER) is an important excision mechanism thatremoves bulky helix-distorting lesions from DNA. Additional detailsabout NER are given in Marteijn 2014, and a summary is given here. NER abroad pathway encompassing two smaller pathways: global genomic NER(GG-NER) and transcription coupled repair NER (TC-NER). GG-NER andTC-NER use different factors for recognizing DNA damage. However, theyutilize the same machinery for lesion incision, repair, and ligation.

Once damage is recognized, the cell removes a short single-stranded DNAsegment that contains the lesion. Endonucleases XPF/ERCC1 and XPG(encoded by ERCC5) remove the lesion by cutting the damaged strand oneither side of the lesion, resulting in a single-strand gap of 22-30nucleotides. Next, the cell performs DNA gap filling synthesis andligation. Involved in this process are: PCNA, RFC, DNA Pol δ, DNA Pol εor DNA Pol κ, and DNA ligase I or XRCC1/Ligase III. Replicating cellstend to use DNA pol F and DNA ligase I, while non-replicating cells tendto use DNA Pol δ, DNA Pol κ, and the XRCC1/Ligase III complex to performthe ligation step.

NER can involve the following factors: XPA-G, POLH, XPF, ERCC1, XPA-G,and LIG1. Transcription-coupled NER (TC-NER) can involve the followingfactors: CSA, CSB, XPB, XPD, XPG, ERCC1, and TTDA. Additional factorsthat may promote the NER repair pathway include XPA-G, POLH, XPF, ERCC1,XPA-G, LIG1, CSA, CSB, XPA, XPB, XPC, XPD, XPF, XPG, TTDA, UVSSA, USP7,CETN2, RAD23B, UV-DDB, CAK subcomplex, RPA, and PCNA.

Interstrand Crosslink (ICL)

A dedicated pathway called the ICL repair pathway repairs interstrandcrosslinks. Interstrand crosslinks, or covalent crosslinks between basesin different DNA strand, can occur during replication or transcription.ICL repair involves the coordination of multiple repair processes, inparticular, nucleolytic activity, translesion synthesis (TLS), and HDR.Nucleases are recruited to excise the ICL on either side of thecrosslinked bases, while TLS and HDR are coordinated to repair the cutstrands. ICL repair can involve the following factors: endonucleases,e.g., XPF and RAD51C, endonucleases such as RAD51, translesionpolymerases, e.g., DNA polymerase zeta and Rev 1), and the Fanconianemia (FA) proteins, e.g., FancJ.

Other Pathways

Several other DNA repair pathways exist in mammals.

Translesion synthesis (TLS) is a pathway for repairing a single strandedbreak left after a defective replication event and involves translesionpolymerases, e.g., DNA polo and Rev 1.

Error-free postreplication repair (PRR) is another pathway for repairinga single stranded break left after a defective replication event.

Target Cells

Cas9 molecules and gRNA molecules, e.g., a Cas9 molecule/gRNA moleculecomplex, can be used to alter (e.g., introduce a mutation in) a targetnucleic acid in a wide variety of cells. This alteration may be carriedout in vitro, ex vivo, or in vivo. In certain embodiments, thisalteration results in modulation of gene expression.

The Cas9 and gRNA molecules described herein can be delivered to atarget cell. Exemplary target cells include, but are not limited to,blood cells, neural cells, immune cells, muscle cells, kidney cells,mammary cells, GI tract cells, vascular cells, lung cells, bone cells,pancreatic cells, skin cells, adipocytes, hormone secreting cells, livercells, epithelial cells, and fibroblasts. In certain embodiments, thetarget cell is a normal cell. In other embodiments, the target cell is adiseased cell. In certain of these embodiments, the target cell is acancer cell.

A suitable cell may include a stem cell such as, e.g., an embryonic stemcell, induced pluripotent stem cell, hematopoietic stem cell, neuronalstem cell, or mesenchymal stem cell. In certain embodiments, the cell isan induced pluripotent stem (iPS) cell or a cell derived from an iPScell, e.g., an iPS cell generated from the subject, modified to correctthe mutation, and differentiated into a clinically relevant cell suchas, e.g., a hepatocyte, macrophage, mononuclear phagocyte, alveolarmacrophage, myeloid progenitor cell, lung epithelial cell, orhematopoietic stem cell. In certain embodiments, AAV is used totransduce the target cells.

Cells produced by the methods described herein may be used immediately.Alternatively, the cells may be frozen (e.g., in liquid nitrogen) andstored for later use. The cells will usually be frozen in 10%dimethylsulfoxide (DMSO), 50% serum, 40% buffered medium, or some othersuch solution as is commonly used in the art to preserve cells at suchfreezing temperature, and thawed in such a manner as commonly known inthe art for thawing frozen cultured cells.

Delivery, Formulations, and Routes of Administration

Cas system components, e.g., a Cas9 molecule, gRNA molecule (e.g., aCas9 molecule/gRNA molecule complex), a donor template nucleic acid, orall three, can be delivered, formulated, or administered in a variety offorms, see, e.g., Tables 3 and 4. Table 3 provides examples of how thecomponents can be formulated, delivered, or administered. Table 4summarizes various delivery methods for the components of a Cas system,e.g., the Cas9 molecule component and the gRNA molecule component, asdescribed herein.

DNA-Based Delivery of Cas9, gRNA, and/or Donor Templates

DNA encoding a Cas9 molecule (e.g., a eaCas9 molecule) or gRNA molecule,a donor template, or any combination thereof (e.g., two or all) can beadministered to subjects or delivered into cells by art-known methods oras described herein. For example, DNA encoding Cas9 and/or gRNA, as wellas donor templates, can be delivered by, e.g., vectors (e.g., viral ornon-viral vectors), non-vector based methods (e.g., using naked DNA orDNA complexes), or a combination thereof. Similarly, donor templates canbe delivered by, e.g., vectors (e.g., viral or non-viral vectors),non-vector based methods (e.g., using naked DNA or DNA complexes), or acombination thereof.

DNA encoding Cas9 molecules (e.g., eaCas9 molecules) and/or gRNAmolecules can be conjugated to molecules (e.g., N-acetylgalactosamine)promoting uptake by the target cells (e.g., the target cells describedherein). Donor templates can likewise be conjugated to molecules (e.g.,N-acetylgalactosamine) promoting uptake by the target cells (e.g., thetarget cells described herein).

In certain embodiments, a DNA encoding Cas9 and/or gRNA is delivered bya vector (e.g., viral vector/virus or plasmid).

In certain embodiments, the vector may comprise a DNA sequence thatencodes a Cas9 molecule and/or a gRNA molecule. In certain embodiments,the vector may comprise a donor template with high homology to theregion (e.g., target sequence) being targeted. In certain of theseembodiments, the donor template comprises all or part of a targetsequence. Exemplary donor templates are a repair template, e.g., a genecorrection template, or a gene mutation template, e.g., point mutation(e.g., single nucleotide (nt) substitution) template).

In certain embodiments, the vector may comprise a sequence encoding asignal peptide (e.g., for nuclear localization, nucleolar localization,or mitochondrial localization), fused, e.g., to a Cas9 moleculesequence. In certain embodiments, the vector may comprise one or moreregulatory/control elements, e.g., promoters, enhancers, introns,polyadenylation signals, Kozak consensus sequences, internal ribosomeentry sites (IRES), 2A sequences, and/or splice acceptors or donors. Incertain of these embodiments wherein the vector comprises a promoter,the promoter is recognized by RNA polymerase II (e.g., a CMV promoter).In other embodiments, the promoter is recognized by RNA polymerase III(e.g., a U6 promoter).

In certain embodiments, the vector is a viral vector (e.g., forgeneration of recombinant viruses). In certain of these embodiments, thevirus is a DNA virus (e.g., dsDNA or ssDNA virus). In other embodiments,the virus is an RNA virus (e.g., an ssRNA virus). Exemplary viralvectors/viruses include, e.g., retroviruses, lentiviruses, adenoviruses,adeno-associated viruses (AAV), vaccinia viruses, poxviruses, and herpessimplex viruses. In certain embodiments, a DNA encoding Cas9 and/or gRNAis delivered by a recombinant AAV. In certain embodiments, a donortemplate nucleic acid is delivered by a recombinant AAV. In certainembodiments, the viral vector is capable of cell type and/or tissue typerecognition. In certain embodiments, the viral vector achieves celltype-specific expression. In certain embodiments, the viral vector hasincreased efficiency of fusion of the viral vector and a target cellmembrane.

In certain embodiments, a DNA encoding Cas9 and/or gRNA is delivered bya non-vector based method (e.g., using naked DNA or DNA complexes). Forexample, the DNA can be delivered, e.g., by organically modified silicaor silicate (Ormosil), electroporation, transient cell compression orsqueezing (see, e.g., Lee 2012), gene gun, sonoporation, magnetofection,lipid-mediated transfection, dendrimers, inorganic nanoparticles,calcium phosphates, or a combination thereof.

In certain embodiments, a DNA encoding Cas9 and/or gRNA is delivered bya combination of vector and non-vector based methods. In certainembodiments, a donor template is delivered by a combination of vectorand non-vector based methods.

Exemplary lipids for gene transfer are shown below in Table 1. Exemplarypolymers for gene transfer are shown below in Table 5.

In certain embodiments, a non-vector delivery vehicle has targetingmodifications to increase target cell update of nanoparticles andliposomes, e.g., cell specific antigens, monoclonal antibodies, singlechain antibodies, aptamers, polymers, sugars (e.g.,N-acetylgalactosamine (GalNAc)), and cell penetrating peptides. Incertain embodiments, the vehicle uses fusogenic andendosome-destabilizing peptides/polymers. In certain embodiments, thevehicle undergoes acid-triggered conformational changes (e.g., toaccelerate endosomal escape of the cargo). In certain embodiments, astimuli-cleavable polymer is used, e.g., for release in a cellularcompartment. In certain embodiments, the delivery vehicle is abiological non-viral delivery vehicle.

In certain embodiments, one or more nucleic acid molecules (e.g., DNAmolecules) other than components of a Cas system (i.e., other than DNAencoding Cas9 molecules and/or gRNA molecules, or donor templates) aredelivered. In certain of these embodiments, these other nucleic acidmolecules are delivered at the same time as one or more of thecomponents of the Cas system. In other embodiments, these other nucleicacid molecules are delivered before or after (e.g., less than about 30minutes, 1 hour, 2 hours, 3 hours, 6 hours, 9 hours, 12 hours, 1 day, 2days, 3 days, 1 week, 2 weeks, or 4 weeks) one or more of the componentsof the Cas system. In certain embodiments, these other nucleic acidmolecules are delivered by a different means than the one or more of thecomponents of the Cas system. The other nucleic acid molecules can bedelivered by any of the delivery methods described herein.

RNA-Based Delivery of Cas9 and or gRNA

gRNA molecules and/or RNA molecules encoding Cas9 molecules can bedelivered into cells, e.g., target cells described herein, by art-knownmethods or as described herein. For example, gRNA molecules and/or RNAmolecules encoding Cas9 molecules can be delivered, e.g., bymicroinjection, electroporation, transient cell compression or squeezing(see, e.g., Lee 2012), lipid-mediated transfection, peptide-mediateddelivery, or a combination thereof gRNA molecules and/or RNA moleculesencoding Cas9 molecules can be conjugated to molecules promoting uptakeby the target cells (e.g., target cells described herein).

In certain embodiments, delivery via electroporation comprises mixingthe cells with the gRNA molecules and/or RNA molecules encoding Cas9molecules, with or without donor template nucleic acid molecules, in acartridge, chamber, or cuvette, and applying one or more electricalimpulses of defined duration and amplitude. In certain embodiments,delivery via electroporation is performed using a system in which cellsare mixed with the gRNA molecules and/or RNA molecules encoding Cas9molecules, with or without donor template nucleic acid molecules, in avessel connected to a device (e.g., a pump) which feeds the mixture intoa cartridge, chamber, or cuvette wherein one or more electrical impulsesof defined duration and amplitude are applied, after which the cells aredelivered to a second vessel. gRNA molecules and/or RNA moleculesencoding Cas9 molecules can be conjugated to molecules to promote uptakeby the target cells (e.g., target cells described herein).

Delivery of Cas9 Molecules

Cas9 molecules can be delivered into cells by art-known methods or asdescribed herein. For example, Cas9 protein molecules can be delivered,e.g., by microinjection, electroporation, transient cell compression orsqueezing (see, e.g., Lee 2012), lipid-mediated transfection,peptide-mediated delivery, or a combination thereof. Delivery can beaccompanied by DNA encoding a gRNA or by a gRNA. Cas9 protein can beconjugated to molecules promoting uptake by the target cells (e.g.,target cells described herein).

In certain embodiments, a Cas9 protein may be combined with a gRNAmolecule to form a ribonucleoprotein (RNP) complex to be administered toa subject or delivered into a cell by art-known methods or as describedherein. Direct delivery of Cas9/gRNA RNP complexes to cells eliminatesthe need to express from nucleic acid (e.g., transfection of plasmidsencoding Cas9 and gRNA). It also eliminates unwanted integration of DNAsegments derived from nucleic acid delivery (e.g., transfection ofplasmids encoding Cas9 and gRNA). Therefore it is an alternativedelivery approach which provides rapid action, fast turnover, high rateof on-target modification, reduced off-target effects, and less toxicityto cells. It can also be utilized to deliver the Cas9/gRNA complex tocells that are difficult to transfect (e.g., primary and pluripotentstem cells that are difficult to transfect). In certain embodiments, aCas9/gRNA RNP complex may be formed prior to administration (i.e.,pre-formed). In certain embodiments, multiple (e.g., more than one)Cas9/gRNA RNP complexes may be delivered (e.g., administered)simultaneously or sequentially. In certain embodiments, Cas9/gRNA RNPcomplexes may be delivered to cells by electroporation.

In certain embodiments, delivery via electroporation comprises mixingthe cells with the Cas9 molecules, with or without gRNA molecules and/ordonor template nucleic acids, in a cartridge, chamber, or cuvette, andapplying one or more electrical impulses of defined duration andamplitude. In certain embodiments, delivery via electroporation isperformed using a system in which cells are mixed with the Cas9molecules with or without gRNA and/or donor template nucleic acids in avessel connected to a device (e.g., a pump) which feeds the mixture intoa cartridge, chamber, or cuvette wherein one or more electrical impulsesof defined duration and amplitude are applied, after which the cells aredelivered to a second vessel.

Route of Administration of Cas System Components

Systemic modes of administration include oral and parenteral routes.Parenteral routes include, by way of example, intravenous,intraarterial, intramuscular, intradermal, subcutaneous, intranasal, andintraperitoneal routes. Components administered systemically may bemodified or formulated to target the components to cells of the bloodand bone marrow.

Local modes of administration include, by way of example, intra-bonemarrow, intrathecal, and intra-cerebroventricular routes. In certainembodiments, significantly smaller amounts of the components (comparedwith systemic approaches) may exert an effect when administered locallycompared to when administered systemically (for example, intravenously).Local modes of administration can reduce or eliminate the incidence ofpotentially toxic side effects that may occur when therapeuticallyeffective amounts of a component are administered systemically.

In addition, components may be formulated to permit release over aprolonged period of time.

Ex Vivo Delivery of Cas System Components

In certain embodiments, Cas system components described in Table 3 areintroduced into cells which are then introduced into a subject, e.g.,the cells are removed from a subject, manipulated ex vivo, andreintroduced into the subject. Methods of introducing the components caninclude, e.g., any of the delivery methods described in Table 4.

Modified Nucleosides, Nucleotides, and Nucleic Acids

Modified nucleosides and modified nucleotides can be present in nucleicacids, e.g., particularly gRNA, but also other forms of RNA, e.g., mRNA,RNAi, or siRNA. As described herein, “nucleoside” is defined as acompound containing a five-carbon sugar molecule (a pentose or ribose)or derivative thereof, and an organic base, purine or pyrimidine, or aderivative thereof. As described herein, “nucleotide” is defined as anucleoside further comprising a phosphate group.

Modified nucleosides and nucleotides can include one or more of:

(i) alteration, e.g., replacement, of one or both of the non-linkingphosphate oxygens and/or of one or more of the linking phosphate oxygensin the phosphodiester backbone linkage;

(ii) alteration, e.g., replacement, of a constituent of the ribosesugar, e.g., of the 2′ hydroxyl on the ribose sugar;

(iii) wholesale replacement of the phosphate moiety with “dephospho”linkers;

(iv) modification or replacement of a naturally occurring nucleobase;

(v) replacement or modification of the ribose-phosphate backbone;

(vi) modification of the 3′ end or 5′ end of the oligonucleotide, e.g.,removal, modification or replacement of a terminal phosphate group orconjugation of a moiety; and

(vii) modification of the sugar.

The modifications listed above can be combined to provide modifiednucleosides and nucleotides that can have two, three, four, or moremodifications. For example, a modified nucleoside or nucleotide can havea modified sugar and a modified nucleobase. In an embodiment, every baseof a gRNA is modified, e.g., all bases have a modified phosphate group,e.g., all are phosphorothioate groups. In an embodiment, all, orsubstantially all, of the phosphate groups of a unimolecular or modulargRNA molecule are replaced with phosphorothioate groups.

In an embodiment, modified nucleotides, e.g., nucleotides havingmodifications as described herein, can be incorporated into a nucleicacid, e.g., a “modified nucleic acid.” In an embodiment, the modifiednucleic acids comprise one, two, three or more modified nucleotides. Inan embodiment, at least 5% (e.g., at least about 5%, at least about 10%,at least about 15%, at least about 20%, at least about 25%, at leastabout 30%, at least about 35%, at least about 40%, at least about 45%,at least about 50%, at least about 55%, at least about 60%, at leastabout 65%, at least about 70%, at least about 75%, at least about 80%,at least about 85%, at least about 90%, at least about 95%, or about100%) of the positions in a modified nucleic acid are a modifiednucleotides.

Unmodified nucleic acids can be prone to degradation by, e.g., cellularnucleases. For example, nucleases can hydrolyze nucleic acidphosphodiester bonds. Accordingly, in one aspect the modified nucleicacids described herein can contain one or more modified nucleosides ornucleotides, e.g., to introduce stability toward nucleases.

In an embodiment, the modified nucleosides, modified nucleotides, andmodified nucleic acids described herein can exhibit a reduced innateimmune response when introduced into a population of cells, both in vivoand ex vivo. The term “innate immune response” includes a cellularresponse to exogenous nucleic acids, including single stranded nucleicacids, generally of viral or bacterial origin, which involves theinduction of cytokine expression and release, particularly theinterferons, and cell death. In an embodiment, the modified nucleosides,modified nucleotides, and modified nucleic acids described herein candisrupt binding of a major groove interacting partner with the nucleicacid. In an embodiment, the modified nucleosides, modified nucleotides,and modified nucleic acids described herein can exhibit a reduced innateimmune response when introduced into a population of cells, both in vivoand ex vivo, and also disrupt binding of a major groove interactingpartner with the nucleic acid.

Definitions of Chemical Groups

As used herein, “alkyl” is meant to refer to a saturated hydrocarbongroup which is straight-chained or branched. Example alkyl groupsinclude methyl (Me), ethyl (Et), propyl (e.g., n-propyl and isopropyl),butyl (e.g., n-butyl, isobutyl, t-butyl), pentyl (e.g., n-pentyl,isopentyl, neopentyl), and the like. An alkyl group can contain from 1to about 20, from 2 to about 20, from 1 to about 12, from 1 to about 8,from 1 to about 6, from 1 to about 4, or from 1 to about 3 carbon atoms.

As used herein, “aryl” refers to monocyclic or polycyclic (e.g., having2, 3 or 4 fused rings) aromatic hydrocarbons such as, for example,phenyl, naphthyl, anthracenyl, phenanthrenyl, indanyl, indenyl, and thelike. In an embodiment, aryl groups have from 6 to about 20 carbonatoms.

As used herein, “alkenyl” refers to an aliphatic group containing atleast one double bond.

As used herein, “alkynyl” refers to a straight or branched hydrocarbonchain containing 2-12 carbon atoms and characterized in having one ormore triple bonds. Examples of alkynyl groups include, but are notlimited to, ethynyl, propargyl, and 3-hexynyl.

As used herein, “arylalkyl” or “aralkyl” refers to an alkyl moiety inwhich an alkyl hydrogen atom is replaced by an aryl group. Aralkylincludes groups in which more than one hydrogen atom has been replacedby an aryl group. Examples of“arylalkyl” or “aralkyl” include benzyl,2-phenylethyl, 3-phenylpropyl, 9-fluorenyl, benzhydryl, and tritylgroups.

As used herein, “cycloalkyl” refers to a cyclic, bicyclic, tricyclic, orpolycyclic non-aromatic hydrocarbon groups having 3 to 12 carbons.Examples of cycloalkyl moieties include, but are not limited to,cyclopropyl, cyclopentyl, and cyclohexyl.

As used herein, “heterocyclyl” refers to a monovalent radical of aheterocyclic ring system. Representative heterocyclyls include, withoutlimitation, tetrahydrofuranyl, tetrahydrothienyl, pyrrolidinyl,pyrrolidonyl, piperidinyl, pyrrolinyl, piperazinyl, dioxanyl,dioxolanyl, diazepinyl, oxazepinyl, thiazepinyl, and morpholinyl.

As used herein, “heteroaryl” refers to a monovalent radical of aheteroaromatic ring system. Examples of heteroaryl moieties include, butare not limited to, imidazolyl, oxazolyl, thiazolyl, triazolyl,pyrrolyl, furanyl, indolyl, thiophenyl pyrazolyl, pyridinyl, pyrazinyl,pyridazinyl, pyrimidinyl, indolizinyl, purinyl, naphthyridinyl,quinolyl, and pteridinyl.

Phosphate Backbone Modifications Phosphate Group

In an embodiment, the phosphate group of a modified nucleotide can bemodified by replacing one or more of the oxygens with a differentsubstituent. Further, the modified nucleotide, e.g., modified nucleotidepresent in a modified nucleic acid, can include the wholesalereplacement of an unmodified phosphate moiety with a modified phosphateas described herein. In an embodiment, the modification of the phosphatebackbone can include alterations that result in either an unchargedlinker or a charged linker with unsymmetrical charge distribution.

Examples of modified phosphate groups include, phosphorothioate,phosphoroselenates, borano phosphates, borano phosphate esters, hydrogenphosphonates, phosphoroamidates, alkyl or aryl phosphonates andphosphotriesters. In an embodiment, one of the non-bridging phosphateoxygen atoms in the phosphate backbone moiety can be replaced by any ofthe following groups: sulfur (S), selenium (Se), BR₃ (wherein R can be,e.g., hydrogen, alkyl, or aryl), C (e.g., an alkyl group, an aryl group,and the like), H, NR₂ (wherein R can be, e.g., hydrogen, alkyl, oraryl), or OR (wherein R can be, e.g., alkyl or aryl). The phosphorousatom in an unmodified phosphate group is achiral. However, replacementof one of the non-bridging oxygens with one of the above atoms or groupsof atoms can render the phosphorous atom chiral; that is to say that aphosphorous atom in a phosphate group modified in this way is astereogenic center. The stereogenic phosphorous atom can possess eitherthe “R” configuration (herein Rp) or the “S” configuration (herein Sp).

Phosphorodithioateshave both non-bridging oxygens replaced by sulfur.The phosphorus center in the phosphorodithioates is achiral whichprecludes the formation of oligoribonucleotide diastereomers. In anembodiment, modifications to one or both non-bridging oxygens can alsoinclude the replacement of the non-bridging oxygens with a groupindependently selected from S, Se, B, C, H, N, and OR (R can be, e.g.,alkyl or aryl).

The phosphate linker can also be modified by replacement of a bridgingoxygen, (i.e., the oxygen that links the phosphate to the nucleoside),with nitrogen (bridged phosphoroamidates), sulfur (bridgedphosphorothioates) and carbon (bridged methylenephosphonates). Thereplacement can occur at either linking oxygen or at both of the linkingoxygens.

Replacement of the Phosphate Group

The phosphate group can be replaced by non-phosphorus containingconnectors. In an embodiment, the charge phosphate group can be replacedby a neutral moiety.

Examples of moieties which can replace the phosphate group can include,without limitation, e.g., methyl phosphonate, hydroxylamino, siloxane,carbonate, carboxymethyl, carbamate, amide, thioether, ethylene oxidelinker, sulfonate, sulfonamide, thioformacetal, formacetal, oxime,methyleneimino, methylenemethylimino, methylenehydrazo,methylenedimethylhydrazo and methyleneoxymethylimino.

Replacement of the Ribophosphate Backbone

Scaffolds that can mimic nucleic acids can also be constructed whereinthe phosphate linker and ribose sugar are replaced by nuclease resistantnucleoside or nucleotide surrogates. In an embodiment, the nucleobasescan be tethered by a surrogate backbone. Examples can include, withoutlimitation, the morpholino, cyclobutyl, pyrrolidine and peptide nucleicacid (PNA) nucleoside surrogates.

Sugar Modifications

The modified nucleosides and modified nucleotides can include one ormore modifications to the sugar group. For example, the 2′ hydroxylgroup (OH) can be modified or replaced with a number of different “oxy”or “deoxy” substituents. In an embodiment, modifications to the 2′hydroxyl group can enhance the stability of the nucleic acid since thehydroxyl can no longer be deprotonated to form a 2′-alkoxide ion. The2′-alkoxide can catalyze degradation by intramolecular nucleophilicattack on the linker phosphorus atom.

Examples of “oxy”-2′ hydroxyl group modifications can include alkoxy oraryloxy (OR, wherein “R” can be, e.g., alkyl, cycloalkyl, aryl, aralkyl,heteroaryl or a sugar); polyethyleneglycols (PEG),O(CH₂CH₂O)_(n)CH₂CH₂OR wherein R can be, e.g., H or optionallysubstituted alkyl, and n can be an integer from 0 to 20 (e.g., from 0 to4, from 0 to 8, from 0 to 10, from 0 to 16, from 1 to 4, from 1 to 8,from 1 to 10, from 1 to 16, from 1 to 20, from 2 to 4, from 2 to 8, from2 to 10, from 2 to 16, from 2 to 20, from 4 to 8, from 4 to 10, from 4to 16, and from 4 to 20). In an embodiment, the “oxy”-2′ hydroxyl groupmodification can include “locked” nucleic acids (LNA) in which the 2′hydroxyl can be connected, e.g., by a C₁₋₆ alkylene or C₁₋₆heteroalkylene bridge, to the 4′ carbon of the same ribose sugar, whereexemplary bridges can include methylene, propylene, ether, or aminobridges; O-amino (wherein amino can be, e.g., NH₂; alkylamino,dialkylamino, heterocyclyl, arylamino, diarylamino, heteroarylamino, ordiheteroarylamino, ethylenediamine, or polyamino) and aminoalkoxy,O(CH₂)_(n)-amino, (wherein amino can be, e.g., NH₂; alkylamino,dialkylamino, heterocyclyl, arylamino, diarylamino, heteroarylamino, ordiheteroarylamino, ethylenediamine, or polyamino). In an embodiment, the“oxy”-2′ hydroxyl group modification can include the methoxyethyl group(MOE), (OCH₂CH₂OCH₃, e.g., a PEG derivative).

“Deoxy” modifications can include hydrogen (i.e., deoxyribose sugars,e.g., at the overhang portions of partially ds RNA); halo (e.g., bromo,chloro, fluoro, oriodo); amino (wherein amino can be, e.g., NH₂;alkylamino, dialkylamino, heterocyclyl, arylamino, diarylamino,heteroarylamino, diheteroarylamino, or amino acid);NH(CH₂CH₂NH)_(n)CH₂CH₂-amino (wherein amino can be, e.g., as describedherein), —NHC(O)R (wherein R can be, e.g., alkyl, cycloalkyl, aryl,aralkyl, heteroaryl or sugar), cyano; mercapto; alkyl-thio-alkyl;thioalkoxy; and alkyl, cycloalkyl, aryl, alkenyl and alkynyl, which maybe optionally substituted with e.g., an amino as described herein.

The sugar group can also contain one or more carbons that possess theopposite stereochemical configuration than that of the correspondingcarbon in ribose. Thus, a modified nucleic acid can include nucleotidescontaining e.g., arabinose, as the sugar. The nucleotide “monomer” canhave an alpha linkage at the 1′ position on the sugar, e.g.,alpha-nucleosides. The modified nucleic acids can also include “abasic”sugars, which lack a nucleobase at C-1′. These abasic sugars can also befurther modified at one or more of the constituent sugar atoms. Themodified nucleic acids can also include one or more sugars that are inthe L form, e.g., L-nucleosides.

Generally, RNA includes the sugar group ribose, which is a 5-memberedring having an oxygen. Exemplary modified nucleosides and modifiednucleotides can include, without limitation, replacement of the oxygenin ribose (e.g., with sulfur (S), selenium (Se), or alkylene, such as,e.g., methylene or ethylene); addition of a double bond (e.g., toreplace ribose with cyclopentenyl or cyclohexenyl); ring contraction ofribose (e.g., to form a 4-membered ring of cyclobutane or oxetane); ringexpansion of ribose (e.g., to form a 6- or 7-membered ring having anadditional carbon or heteroatom, such as for example, anhydrohexitol,altritol, mannitol, cyclohexanyl, cyclohexenyl, and morpholino that alsohas a phosphoramidate backbone). In an embodiment, the modifiednucleotides can include multicyclic forms (e.g., tricyclo; and“unlocked” forms, such as glycol nucleic acid (GNA) (e.g., R-GNA orS-GNA, where ribose is replaced by glycol units attached tophosphodiester bonds), threose nucleic acid (TNA, where ribose isreplaced with α-L-threofuranosyl-(3′→2′)).

Modifications on the Nucleobase

The modified nucleosides and modified nucleotides described herein,which can be incorporated into a modified nucleic acid, can include amodified nucleobase. Examples of nucleobases include, but are notlimited to, adenine (A), guanine (G), cytosine (C), and uracil (U).These nucleobases can be modified or wholly replaced to provide modifiednucleosides and modified nucleotides that can be incorporated intomodified nucleic acids. The nucleobase of the nucleotide can beindependently selected from a purine, a pyrimidine, a purine orpyrimidine analog. In an embodiment, the nucleobase can include, forexample, naturally-occurring and synthetic derivatives of a base.

Uracil

In an embodiment, the modified nucleobase is a modified uracil.Exemplary nucleobases and nucleosides having a modified uracil includewithout limitation pseudouridine (W), pyridin-4-one ribonucleoside,5-aza-uridine, 6-aza-uridine, 2-thio-5-aza-uridine, 2-thio-uridine(s2U), 4-thio-uridine (s4U), 4-thio-pseudouridine, 2-thio-pseudouridine,5-hydroxy-uridine (ho⁵U), 5-aminoallyl-uridine, 5-halo-uridine (e.g.,5-iodo-uridine or 5-bromo-uridine), 3-methyl-uridine (m³U),5-methoxy-uridine (mo⁵U), uridine 5-oxyacetic acid (cmo⁵U), uridine5-oxyacetic acid methyl ester (mcmo⁵U), 5-carboxymethyl-uridine (cm⁵U),1-carboxymethyl-pseudouridine, 5-carboxyhydroxymethyl-uridine (chm⁵U),5-carboxyhydroxymethyl-uridine methyl ester (mchm⁵U), 5-methoxycarbonylmethyl-uridine (mcm⁵U), 5-methoxycarbonylmethyl-2-thio-uridine(mcm⁵s2U), 5-aminomethyl-2-thio-uridine (nm⁵s2U),5-methylaminomethyl-uridine (mnm⁵U), 5-methylaminomethyl-2-thio-uridine(mnm⁵s2U), 5-methylaminomethyl-2-seleno-uridine (mnm⁵se²U),5-carbamoylmethyl-uridine (ncm⁵U), 5-carboxymethylaminomethyl-uridine(cmnm⁵U), 5-carboxymethylaminomethyl-2-thio-uridine (cmnm⁵s2U),5-propynyl-uridine, 1-propynyl-pseudouridine, 5-taurinomethyl-uridine(τcm⁵U), 1-taurinomethyl-pseudouridine,5-taurinomethyl-2-thio-uridine(τm⁵s2U),1-taurinomethyl-4-thio-pseudouridine, 5-methyl-uridine (m⁵U, i.e.,having the nucleobase deoxythymine), 1-methyl-pseudouridine (m¹ψ),5-methyl-2-thio-uridine (m⁵s2U), 1-methyl-4-thio-pseudouridine (m¹s⁴ψ),4-thio-1-methyl-pseudouridine, 3-methyl-pseudouridine (m³ψ),2-thio-1-methyl-pseudouridine, 1-methyl-1-deaza-pseudouridine,2-thio-1-methyl-1-deaza-pseudouridine, dihydrouridine (D),dihydropseudouridine, 5,6-dihydrouridine, 5-methyl-dihydrouridine (m⁵D),2-thio-dihydrouridine, 2-thio-dihydropseudouridine, 2-methoxy-uridine,2-methoxy-4-thio-uridine, 4-methoxy-pseudouridine,4-methoxy-2-thio-pseudouridine, N1-methyl-pseudouridine,3-(3-amino-3-carboxypropyl)uridine (acp³U),1-methyl-3-(3-amino-3-carboxypropyl)pseudouridine (acp³ψ),5-(isopentenylaminomethyl)uridine (inm⁵U),5-(isopentenylaminomethyl)-2-thio-uridine (inm⁵s2U), α-thio-uridine,2′-O-methyl-uridine (Um), 5,2′-O-dimethyl-uridine (m⁵Um),2′-O-methyl-pseudouridine (ψm), 2-thio-2′-O-methyl-uridine (s2Um),5-methoxycarbonylmethyl-2′-O-methyl-uridine (mcm³Um),5-carbamoylmethyl-2′-O-methyl-uridine (ncm⁵Um),5-carboxymethylaminomethyl-2′-O-methyl-uridine (cmnm⁵Um),3,2′-O-dimethyl-uridine (m³Um),5-(isopentenylaminomethyl)-2′-O-methyl-uridine (inm⁵Um), 1-thio-uridine,deoxythymidine, 2′-F-ara-uridine, 2′-F-uridine, 2′-OH-ara-uridine,5-(2-carbomethoxyvinyl) uridine, 5-[3-(1-E-propenylamino)uridine,pyrazolo[3,4-d]pyrimidines, xanthine, and hypoxanthine.

Cytosine

In an embodiment, the modified nucleobase is a modified cytosine.Exemplary nucleobases and nucleosides having a modified cytosine includewithout limitation 5-aza-cytidine, 6-aza-cytidine, pseudoisocytidine,3-methyl-cytidine (m³C), N4-acetyl-cytidine (act), 5-formyl-cytidine(f⁵C), N4-methyl-cytidine (m⁴C), 5-methyl-cytidine (m⁵C),5-halo-cytidine (e.g., 5-iodo-cytidine), 5-hydroxymethyl-cytidine(hm⁵C), 1-methyl-pseudoisocytidine, pyrrolo-cytidine,pyrrolo-pseudoisocytidine, 2-thio-cytidine (s2C),2-thio-5-methyl-cytidine, 4-thio-pseudoisocytidine,4-thio-1-methyl-pseudoisocytidine,4-thio-1-methyl-1-deaza-pseudoisocytidine,1-methyl-1-deaza-pseudoisocytidine, zebularine, 5-aza-zebularine,5-methyl-zebularine, 5-aza-2-thio-zebularine, 2-thio-zebularine,2-methoxy-cytidine, 2-methoxy-5-methyl-cytidine,4-methoxy-pseudoisocytidine, 4-methoxy-1-methyl-pseudoisocytidine,lysidine (k²C), α-thio-cytidine, 2′-O-methyl-cytidine (Cm),5,2′-O-dimethyl-cytidine (m⁵Cm), N4-acetyl-2′-O-methyl-cytidine (ac⁴Cm),N4,2′-O-dimethyl-cytidine (m⁴Cm), 5-formyl-2′-O-methyl-cytidine (f⁵Cm),N4,N4,2′-O-trimethyl-cytidine (m⁴²Cm), 1-thio-cytidine,2′-F-ara-cytidine, 2′-F-cytidine, and 2′-OH-ara-cytidine.

Adenine

In an embodiment, the modified nucleobase is a modified adenine.Exemplary nucleobases and nucleosides having a modified adenine includewithout limitation 2-amino-purine, 2,6-diaminopurine,2-amino-6-halo-purine (e.g., 2-amino-6-chloro-purine), 6-halo-purine(e.g., 6-chloro-purine), 2-amino-6-methyl-purine, 8-azido-adenosine,7-deaza-adenosine, 7-deaza-8-aza-adenosine, 7-deaza-2-amino-purine,7-deaza-8-aza-2-amino-purine, 7-deaza-2,6-diaminopurine,7-deaza-8-aza-2,6-diaminopurine, 1-methyl-adenosine (m¹A),2-methyl-adenosine (m²A), N6-methyl-adenosine (m⁶A),2-methylthio-N6-methyl-adenosine (ms2 m⁶A), N6-isopentenyl-adenosine(i⁶A), 2-methylthio-N6-isopentenyl-adenosine (ms²i⁶A),N6-(cis-hydroxyisopentenyl)adenosine (io⁶A),2-methylthio-N6-(cis-hydroxyisopentenyl)adenosine (ms2io⁶A),N6-glycinylcarbamoyl-adenosine (g⁶A), N6-threonylcarbamoyl-adenosine(tA), N6-methyl-N6-threonylcarbamoyl-adenosine (m⁶t⁶A),2-methylthio-N6-threonylcarbamoyl-adenosine (ms²g⁶A),N6,N6-dimethyl-adenosine (m⁶²A), N6-hydroxynorvalylcarbamoyl-adenosine(hn⁶A), 2-methylthio-N6-hydroxynorvalylcarbamoyl-adenosine (m⁶ ₂hn⁶A),N6-acetyl-adenosine (ac⁶A), 7-methyl-adenosine, 2-methylthio-adenosine,2-methoxy-adenosine, α-thio-adenosine, 2′-O-methyl-adenosine (Am),N⁶,2′-O-dimethyl-adenosine (m⁶Am), N⁶-Methyl-2′-deoxyadenosine,N6,N6,2′-O-trimethyl-adenosine (m⁶²Am), 1,2′-O-dimethyl-adenosine(m¹Am), 2′-O-ribosyladenosine (phosphate) (Ar(p)),2-amino-N6-methyl-purine, 1-thio-adenosine, 8-azido-adenosine,2′-F-ara-adenosine, 2′-F-adenosine, 2′-OH-ara-adenosine, andN6-(19-amino-pentaoxanonadecyl)-adenosine.

Guanine

In an embodiment, the modified nucleobase is a modified guanine.Exemplary nucleobases and nucleosides having a modified guanine includewithout limitation inosine (I), 1-methyl-inosine (m¹I), wyosine (imG),methylwyosine (mimG), 4-demethyl-wyosine (imG-14), isowyosine (imG2),wybutosine (yW), peroxywybutosine (o₂yW), hydroxywybutosine (OHyW),undermodified hy droxywybutosine (OHyW*), 7-deaza-guanosine, queuosine(Q), epoxyqueuosine (oQ), galactosyl-queuosine (galQ),mannosyl-queuosine (manQ), 7-cyano-7-deaza-guanosine (preQ₀),7-aminomethyl-7-deaza-guanosine (preQ₁), archaeosine (G+),7-deaza-8-aza-guanosine, 6-thio-guanosine, 6-thio-7-deaza-guanosine,6-thio-7-deaza-8-aza-guanosine, 7-methyl-guanosine (m⁷G),6-thio-7-methyl-guanosine, 7-methyl-inosine, 6-methoxy-guanosine,1-methyl-guanosine (m′G), N2-methyl-guanosine (m²G),N2,N2-dimethyl-guanosine (m² ₂G), N2,7-dimethyl-guanosine (m²,7G),N2,N2,7-dimethyl-guanosine (m²,2,7G), 8-oxo-guanosine,7-methyl-8-oxo-guanosine, 1-methyl-6-thio-guanosine,N2-methyl-6-thio-guanosine, N2,N2-dimethyl-6-thio-guanosine,α-thio-guanosine, 2′-O-methyl-guanosine (Gm),N2-methyl-2′-O-methyl-guanosine (m²Gm),N2,N2-dimethyl-2′-O-methyl-guanosine (m²²Gm),1-methyl-2′-O-methyl-guanosine (m′Gm),N2,7-dimethyl-2′-O-methyl-guanosine (m²,7Gm), 2′-O-methyl-inosine (Im),1,2′-O-dimethyl-inosine (m′Im), O⁶-phenyl-2′-deoxyinosine,2′-O-ribosylguanosine (phosphate) (Gr(p)), 1-thio-guanosine,O⁶-methyl-guanosine, O⁶-Methyl-2′-deoxyguanosine, 2′-F-ara-guanosine,and 2′-F-guanosine.

Exemplary Modified gRNAs

In certain embodiments, modified nucleic acids as described herein canbe modified gRNAs. It is to be understood that any of the gRNAsdescribed herein can be modified as described herein.

Through experimentation (results not shown), it has been found that thegRNA component of the CRISPR/Cas system is more efficient at editinggenes in T cells when the gRNA is modified at or near its 5′ end (e.g.,when the 5′ end of the gRNA is modified by inclusion of a eukaryoticmRNA cap structure or cap analog. While not wishing to be bound bytheory, it is believed that these and other modified gRNAs describedherein elicit a reduced innate immune response from certain circulatorycell types (e.g., T cells), and that this reduced response may beresponsible for the observed improvements. The present inventionencompasses the realization that minimizing the innate immune responseof circulating cells (e.g., T cells) to gRNAs could be advantageous whenusing gRNAs to edit circulating cells (whether ex vivo or in vivo), andcould also be advantageous when using gRNAs to edit non-circulatingcells, e.g., when a gRNA is administered systemically or locally for invivo gene editing purposes. The present invention also encompasses therealization that the improvements observed with a 5′ capped gRNA can beextended to gRNAs that have been modified in other ways to achieve thesame type of structural or functional result (e.g., by the inclusion ofmodified nucleosides or nucleotides, or when an in vitro transcribedgRNA is modified by treatment with a phosphatase such as calf intestinalalkaline phosphatase to remove the 5′ triphosphate group). While notwishing to be bound by theory, in certain embodiments the modified gRNAsdescribed herein may contain one or more modifications (e.g., modifiednucleosides or nucleotides) which introduce stability toward nucleases(e.g., by the inclusion of modified nucleosides or nucleotides and/or a3′ polyA tract).

Accordingly, in certain embodiments the compositions and methodsprovided herein utilize gRNAs that include one or more modifiednucleosides or nucleotides as described herein. In certain of theseembodiments, the inclusion of the one or more modified nucleosides ornucleotides causes the gRNA to elicit a reduced innate immune responsein certain circulating cell types (e.g., T cells, macrophages, dendriticcells, and/or B cells) as compared to an otherwise unmodified gRNA.

In certain embodiments, a gRNA for use in the compositions and methodsprovided herein is modified at or near its 5′ end (e.g., within 1-10,1-5, or 1-2 nucleotides of its 5′ end).

In certain embodiments, the gRNA is modified by inclusion of aeukaryotic mRNA cap structure or cap analog (e.g., a G(5′)ppp(5)G capanalog, a m7G(5′)ppp(5′)G cap analog, or a 3′-O-Me-m7G(5)ppp(5)G antireverse cap analog (ARCA)). The cap or cap analog can incorporatedduring chemical synthesis or in vitro transcription of the gRNA. Incertain embodiments, an in vitro transcribed gRNA is modified bytreatment with a phosphatase (e.g., calf intestinal alkalinephosphatase) to remove the 5′ triphosphate group.

In certain embodiments, a gRNA for use in the compositions and methodsprovided herein is modified at or near its 3′ end (e.g., within 1-10,1-5, or 1-2 nucleotides of its 3′ end).

In an embodiment, the 3′ end of a gRNA is modified by the addition ofone or more (e.g., 25-200) adenine (A) residues. The polyA tract can becontained in the nucleic acid (e.g., plasmid, PCR product, viral genome)encoding the gRNA, or can be added to the gRNA during chemicalsynthesis, or following in vitro transcription using a polyadenosinepolymerase (e.g., E. coli Poly(A)Polymerase).

In certain embodiments, a gRNA for use in the compositions and methodsprovided herein comprises both a modification at or near its 5′ end anda modification at or near its 3′ end.

In certain embodiments, in vitro transcribed gRNA contains both a 5′ capstructure or cap analog and a 3′ polyA tract. In an embodiment, an invitro transcribed gRNA is modified by treatment with a phosphatase(e.g., calf intestinal alkaline phosphatase) to remove the 5′triphosphate group and comprises a 3′ polyA tract.

In some embodiments, gRNAs can be modified at a 3′ terminal U ribose.For example, the two terminal hydroxyl groups of the U ribose can beoxidized to aldehyde groups and a concomitant opening of the ribose ringto afford a modified nucleoside as shown below:

wherein “U” can be an unmodified or modified uridine.

In another embodiment, the 3′ terminal U can be modified with a 2′3′cyclic phosphate as shown below:

wherein “U” can be an unmodified or modified uridine.

In some embodiments, the gRNA molecules may contain 3′ nucleotides whichcan be stabilized against degradation, e.g., by incorporating one ormore of the modified nucleotides described herein. In this embodiment,e.g., uridines can be replaced with modified uridines, e.g.,5-(2-amino)propyl uridine, and 5-bromo uridine, or with any of themodified uridines described herein; adenosines and guanosines can bereplaced with modified adenosines and guanosines, e.g., withmodifications at the 8-position, e.g., 8-bromo guanosine, or with any ofthe modified adenosines or guanosines described herein.

In some embodiments, sugar-modified ribonucleotides can be incorporatedinto the gRNA, e.g., wherein the 2′ OH-group is replaced by a groupselected from H, —OR, —R (wherein R can be, e.g., alkyl, cycloalkyl,aryl, aralkyl, heteroaryl or sugar), halo, —SH, —SR (wherein R can be,e.g., alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or sugar), amino(wherein amino can be, e.g., NH₂; alkylamino, dialkylamino,heterocyclyl, arylamino, diarylamino, heteroarylamino,diheteroarylamino, or amino acid); or cyano (—CN). In some embodiments,the phosphate backbone can be modified as described herein, e.g., with aphosphothioate group. In some embodiments, one or more of thenucleotides of the gRNA can each independently be a modified orunmodified nucleotide including, but not limited to 2′-sugar modified,such as, 2′-O-methyl, 2′-O-methoxyethyl, or 2′-Fluoro modifiedincluding, e.g., 2′-F or 2′-O-methyl, adenosine (A), 2′-F or2′-O-methyl, cytidine (C), 2′-F or 2′-O-methyl, uridine (U), 2′-F or2′-O-methyl, thymidine (T), 2′-F or 2′-O-methyl, guanosine (G),2′-O-methoxyethyl-5-methyluridine (Teo), 2′-O-methoxyethyladenosine(Aeo), 2′-O-methoxyethyl-5-methylcytidine (m5Ceo), and any combinationsthereof.

In some embodiments, a gRNA can include “locked” nucleic acids (LNA) inwhich the 2′ OH-group can be connected, e.g., by a C1-6 alkylene or C1-6heteroalkylene bridge, to the 4′ carbon of the same ribose sugar, whereexemplary bridges can include methylene, propylene, ether, or aminobridges; O-amino (wherein amino can be, e.g., NH₂; alkylamino,dialkylamino, heterocyclyl, arylamino, diarylamino, heteroarylamino, ordiheteroarylamino, ethylenediamine, or polyamino) and aminoalkoxy orO(CH₂)_(n)-amino (wherein amino can be, e.g., NH₂; alkylamino,dialkylamino, heterocyclyl, arylamino, diarylamino, heteroarylamino, ordiheteroarylamino, ethylenediamine, or polyamino).

In some embodiments, a gRNA can include a modified nucleotide which ismulticyclic (e.g., tricyclo; and “unlocked” forms, such as glycolnucleic acid (GNA) (e.g., R-GNA or S-GNA, where ribose is replaced byglycol units attached to phosphodiester bonds), or threose nucleic acid(TNA, where ribose is replaced with α-L-threofuranosyl-(3′→2′)).

Generally, gRNA molecules include the sugar group ribose, which is a5-membered ring having an oxygen. Exemplary modified gRNAs can include,without limitation, replacement of the oxygen in ribose (e.g., withsulfur (S), selenium (Se), or alkylene, such as, e.g., methylene orethylene); addition of a double bond (e.g., to replace ribose withcyclopentenyl or cyclohexenyl); ring contraction of ribose (e.g., toform a 4-membered ring of cyclobutane or oxetane); ring expansion ofribose (e.g., to form a 6- or 7-membered ring having an additionalcarbon or heteroatom, such as for example, anhydrohexitol, altritol,mannitol, cyclohexanyl, cyclohexenyl, and morpholino that also has aphosphoramidate backbone). Although the majority of sugar analogalterations are localized to the 2′ position, other sites are amenableto modification, including the 4′ position. In an embodiment, a gRNAcomprises a 4′-S, 4′-Se or a 4′-C-aminomethyl-2′-O-Me modification.

In some embodiments, deaza nucleotides, e.g., 7-deaza-adenosine, can beincorporated into the gRNA. In some embodiments, O- and N-alkylatednucleotides, e.g., N6-methyl adenosine, can be incorporated into thegRNA. In some embodiments, one or more or all of the nucleotides in agRNA molecule are deoxynucleotides.

miRNA Binding Sites

microRNAs (or miRNAs) are naturally occurring cellular 19-25 nucleotidelong noncoding RNAs. They bind to nucleic acid molecules having anappropriate miRNA binding site, e.g., in the 3′ UTR of an mRNA, anddown-regulate gene expression. While not wishing to be bound by theory,itis believed that this down regulation occurs by either reducingnucleic acid molecule stability or inhibiting translation. An RNAspecies disclosed herein, e.g., an mRNA encoding Cas9, can comprise anmiRNA binding site, e.g., in its 3′UTR. The miRNA binding site can beselected to promote down regulation of expression is a selected celltype.

EXAMPLES

The following Examples are merely illustrative and are not intended tolimit the scope or content of the invention in any way.

Example 1: Biophysical Characterization and Direct Delivery of Cas9Ribonucleoprotein Complexes

Direct delivery of Cas9 ribonucleoprotein (RNP) complexes allows forefficient gene editing while minimizing off-target activity owing to therapid turnover of the Cas9 protein in cells. The efficiency of geneediting mediated by RNP delivery varies by locus, and depends on thelength of gRNA and the amount and ratio of Cas9 protein and gRNAdelivered.

Structural and biophysical characterization of Cas9 complexes with gRNArevealed a large contact area and a high affinity. Thermal melt curvesare a useful property to detect the binding and stability of complexes.The large increase in melting temperature from an apo-Cas9 molecule(i.e., a Cas9 molecule in the absence of gRNA molecule) to a Cas9molecule complexed with gRNA was used to characterize the affinity ofCas9 for gRNA. Multiple gRNAs of differing lengths were complexed withCas9 at different stoichiometries, and the interaction was measuredusing thermal shift (e.g., the shift of melting temperature). Thesebiophysically characterized complexes were then transfected into 293Tcells, and the efficiency of indel generated was measured. Subtledifferences in gRNA length and base composition was shown to affect thebinding and formation of RNP complex. Correlating binding affinity withefficiency of genome editing allows for the design of an optimalcomposition of RNPs, e.g., for cationic lipid mediated direct delivery.

Evaluation of Cas9 Molecule and Cas9 Molecule/gRNA Molecule Complexes byDSF

S. aureus and S. pyogenes Cas9 molecules were recombinantly expressedand purified using Ni affinity chromatography, SP Sepharose, andSuperdex 200.

DSF was used to examine the stability of purified S. aureus and S.pyogenes Cas9 molecules in the absence of gRNA molecules. The reactionmix contained 5 μM Cas9 molecules and 5× SYPRO Orange® (LifeTechnologies cat #S-6650) in 10 μL volume. The gradient was run at 20°C. for 1 minute, then from 20° C. to 95° C. with 1° C. increments every10 seconds. The derivative of the fluorescent signal was plotted againsttemperature, and the temperature midpoint for the unfolding transition(T_(m)) was determined. As shown in FIGS. 9A and 9B, the S. aureus Cas9molecule (T_(m)=36° C.) was less stable than the S. pyogenes Cas9molecule (T_(m)=40° C.).

DSF was also used to examine Cas9 molecule/gRNA molecule complexes. S.pyogenes Cas9 alone, S. pyogenes Cas9 with 1 μM S. pyogenes gRNA, and S.pyogenes Cas9 with 1 μM S. aureus gRNA were tested in H150 (10 mM HepespH 7.5, 150 mM NaCl). The DNA sequences encoding the gRNA molecules usedin these experiments were:

S. pyogenes gRNA:

(SEQ ID NO: 206) GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGC TTTT; and

S. aureus gRNA:

(SEQ ID NO: 207) GTTTTAGTACTCTGGAAACAGAATCTACTAAAACAAGGCAAAATGCCGTGTTTATCTCGTCAACTTGTTGGCGAGA TTTT.

As shown in FIG. 10, thermal denaturation of the S. pyogenes Cas9 was42° C., and a thermal shift to 50° C. was observed in the presence ofthe concomitant gRNA molecule. However, a shift was not observed whenthe S. pyogenes Cas9 was incubated with an alien gRNA molecule. Theseresults suggest that Cas9 molecule/gRNA molecule complex formation maycorrelate with thermal shift.

Delivery of Cas9 Molecule gRNA Molecule Complexes to Jurkat T Cells

Cas9 and gRNA were at a 1:25 ratio. gRNA construct was generated using aPCR protocol. gRNA was in vitro transcribed and capped (e.g., 5′Anti-Reverse Cap Analog (ARCA) cap) and tailed (e.g., a 3′ polyA tail).As shown in FIG. 11A, gRNA binding induced T_(m) shift from 32° C. to46° C. The Cas9/gRNA complex was delivered to Jurkat T cells. FIG. 11Bindicates that about 20% of the cells loss the CD3 marker.

Example 2: Comparison of gRNA Molecules from In Vitro Transcription orChemical Synthesis

DSF was used to assay the successful formation of Cas9 molecule/gRNAmolecule complex, and the quality and integrity of gRNA moleculesobtained from three methods or suppliers were compared.

gRNA molecules with sequences corresponding to those in Table 6 wereobtained at the 15-50 μg scale.

Purified Cas9 protein at 4 μM was complexed with an equimolar amount ofgRNA at room temperature in H150 buffer (10 mM Hepes pH7.5, 150 mMNaCl). Part of this reaction containing Cas9 molecule/gRNA moleculecomplex (RNP) was then transfected using lipofectamine-2000 transfectionreagent into HEK293FT cells. RNP at 100 nM was used in all cases,regardless of guide source. In each case, the remainder of RNP wasdiluted to 1 μM in H150 buffer, SYPRO orange was added to a finalconcentration of 5× from a 5000× stock, and the DSF assay was performedaccording to assay 1 described herein. Indel quantitation was performedaccording to protocols described herein.

Results of the experiment are summarized in Table 6. Delta T_(m)s werecompared to Cas9 protein melting at 42° C. The results showed thatsamples which indicated complete RNP complex formation as evidenced by aDelta T_(m) of 8-9° C. all showed good NHEJ activity in HEK293FT cells.

Chemically synthesized gRNAs from Company 2 were found inadequate, withnegligible Delta T_(m)s and lower NHEJ activity (11% indels).

In vitro transcribed gRNAs by the MEGAshortscript T7 kit and gRNAspurchased from Company 1 were of sufficient quality and integrity asdemonstrated by 7-8° C. T_(m)s and NHEJ activity in the 22-27° C. range.

Example 3: Cloning and Initial Screening of gRNAs

This example discloses a method for evaluating chimeric gRNAs. The sameapproach may also be used to evaluate modular gRNAs.

Cloning gRNAs into Vectors

For each gRNA, a pair of overlapping oligonucleotides is designed andobtained. Oligonucleotides are annealed and ligated into a digestedvector backbone containing an upstream U6 promoter and the remainingsequence of a long chimeric gRNA. Plasmids are sequence-verified andprepped to generate sufficient amounts of transfection-quality DNA. Incertain embodiments, the U6 promoter may be replaced with an alternatepromoter to drive in vivo transcription (e.g., H1 promoter) or in vitrotranscription (e.g., a T7 promoter).

Cloning gRNAs into Linear dsDNA Molecules (STITCHR)

A single oligonucleotide is designed and obtained for each gRNA. The U6promoter and the gRNA scaffold (e.g., including everything except thetargeting domain, e.g., including sequences derived from the crRNA andtracrRNA, e.g., including a first complementarity domain; a linkingdomain; a second complementarity domain; a proximal domain; and a taildomain) are separately PCR amplified and purified as dsDNA molecules.The gRNA-specific oligonucleotide is used in a PCR reaction to stitchtogether the U6 and the gRNA scaffold, linked by the targeting domainspecified in the oligonucleotide. The resulting dsDNA molecules (STITCHRproducts) are purified for transfection. Any gRNA scaffold may be usedto create gRNAs compatible with Cas9s from any bacterial species. Incertain embodiments, the U6 promoter may be replaced with an alternatepromoter to drive in vivo transcription (e.g., H1 promoter) or in vitrotranscription (e.g., T7 promoter).

Initial gRNA Screen

Each gRNA to be tested is transfected, along with a plasmid expressingCas9 and a small amount of a GFP-expressing plasmid, into human cells.In preliminary experiments, these cells can be immortalized human celllines such as 293T, K562 or U2OS. Alternatively, primary human cells maybe used. The cells used for screening may be relevant to the eventualtherapeutic cell target (e.g., an erythroid cell). The use of primarycells similar to the potential therapeutic target cell population mayprovide important information on gene targeting rates in the context ofendogenous chromatin and gene expression.

Transfection may be performed using lipid transfection (such asLipofectamine or Fugene) or by electroporation (such as LonzaNucleofection). Following transfection, GFP expression can be determinedeither by fluorescence microscopy or by flow cytometry to confirmconsistent and high levels of transfection. Preliminary transfectionscan comprise different gRNAs and different targeting approaches (e.g.,17-mers, 20-mers, nuclease, dual-nickase, etc.) to determine whichgRNAs/combinations of gRNAs give the greatest activity.

Efficiency of cleavage with each gRNA may be assessed by measuringNHEJ-induced indel formation at the target locus by T7E1 endonucleaseassay. For this assay, PCR amplicons are approximately 500-700 bp, withthe intended cut site placed asymmetrically in the amplicon. Followingamplification, purification, and size-verification of PCR products, DNAis denatured and re-hybridized by heating to 95° C. and then slowlycooling. Hybridized PCR products are then digested with T7 EndonucleaseI (or other mismatch-sensitive enzyme), which recognizes and cleavesnon-perfectly matched DNA. If indels are present in the originaltemplate DNA, denaturation and re-annealing of the amplicons results inhybridization of DNA strands harboring different indels, leading todouble-stranded DNA that is not perfectly matched. Digestion productsmay be visualized by gel electrophoresis or capillary electrophoresis.The fraction of DNA that is cleaved (density of cleavage productsdivided by the density of cleaved and uncleaved) may be used to estimatepercent NHEJ using the following equation: % NHEJ=(1-(1-fractioncleaved)^(1/2)). The T7E1 assay is sensitive down to about 2-5% NHEJ.

In certain embodiments, other methods may be used to assess cleavageefficiency, including for example sequencing and use ofmismatch-sensitive enzymes, e.g., Cell/Surveyor nuclease. For Sangersequencing, purified PCR amplicons are cloned into a plasmid backbone,transformed, miniprepped and sequenced with a single primer. Sangersequencing may be used for determining the exact nature of indels afterdetermining the NHEJ rate by T7E1. For next-generation sequencing,amplicons may be 300-500 bp, with the intended cut site placedasymmetrically. Following PCR, next-generation sequencing adapters andbarcodes (for example Illumina multiplex adapters and indexes) may beadded to the ends of the amplicon, e.g., for use in high throughputsequencing (for example on an Illumina MiSeq). This method allows fordetection of very low NHEJ rates.

Example 4: Assessment of Gene Targeting by NHEJ

The gRNAs that induce the greatest levels of NHEJ in initial tests canbe selected for further evaluation of gene targeting efficiency. In thiscase, cells are derived from disease subjects and, therefore, harbor therelevant mutation.

Following transfection (usually 2-3 days post-transfection,) genomic DNAmay be isolated from a bulk population of transfected cells and PCR maybe used to amplify the target region. Following PCR, gene targetingefficiency to generate the desired mutations (either knockout of atarget gene or removal of a target sequence motif) may be determined bysequencing. For Sanger sequencing, PCR amplicons may be 500-700 bp long.For next generation sequencing, PCR amplicons may be 300-500 bp long. Ifthe goal is to knockout gene function, sequencing may be used to assesswhat percent of alleles have undergone NHEJ-induced indels that resultin a frameshift or large deletion or insertion that would be expected todestroy gene function. If the goal is to remove a specific sequencemotif, sequencing may be used to assess what percent of alleles haveundergone NHEJ-induced deletions that span this sequence.

Example 5: Assessment of Gene Targeting by HDR

The gRNAs that induce the greatest levels of NHEJ in initial tests canbe selected for further evaluation of gene targeting efficiency. In thiscase, cells are derived from disease subjects and, therefore, harbor therelevant mutation.

Following transfection (usually 2-3 days post-transfection,) genomic DNAmay be isolated from a bulk population of transfected cells and PCR maybe used to amplify the target region. Following PCR, gene targetingefficiency can be determined by several methods.

Determination of gene targeting frequency involves measuring thepercentage of alleles that have undergone homologous directed repair(HDR) with the exogenously provided donor template or endogenous genomicdonor sequence and which therefore have incorporated the desiredcorrection. If the desired HDR event creates or destroys a restrictionenzyme site, the frequency of gene targeting may be determined by a RFLPassay. If no restriction site is created or destroyed, sequencing may beused to determine gene targeting frequency. If a RFLP assay is used,sequencing may still be used to verify the desired HDR event and ensurethat no other mutations are present. If an exogenously provided donortemplate is employed, at least one of the primers is placed in theendogenous gene sequence outside of the region included in the homologyarms, which prevents amplification of donor template still present inthe cells. Therefore, the length of the homology arms present in thedonor template may affect the length of the PCR amplicon. PCR ampliconscan either span the entire donor region (both primers placed outside thehomology arms) or they can span only part of the donor region and asingle junction between donor and endogenous DNA (one internal and oneexternal primer). If the amplicons span less than the entire donorregion, two different PCRs should be used to amplify and sequence boththe 5′ and the 3′ junction.

If the PCR amplicon is short (less than 600 bp) it is possible to usenext generation sequencing. Following PCR, next generation sequencingadapters and barcodes (for example Illumina multiplex adapters andindexes) may be added to the ends of the amplicon, e.g., for use in highthroughput sequencing (for example on an Illumina MiSeq). This methodallows for detection of very low gene targeting rates.

If the PCR amplicon is too long for next generation sequencing, Sangersequencing can be performed. For Sanger sequencing, purified PCRamplicons will be cloned into a plasmid backbone (for example, TOPOcloned using the LifeTech Zero Blunt© TOPO© cloning kit), transformed,miniprepped and sequenced.

The same or similar assays described above can be used to measure thepercentage of alleles that have undergone HDR with endogenous genomicdonor sequence and which therefore have incorporated the desiredcorrection.

INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned herein arehereby incorporated by reference in their entirety as if each individualpublication, patent or patent application was specifically andindividually indicated to be incorporated by reference. In case ofconflict, the present application, including any definitions herein,will control.

EQUIVALENTS

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents to the specificembodiments of the invention described herein. Such equivalents areintended to be encompassed by the following claims.

REFERENCES

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TABLE 1 Lipids used for gene transfer Lipid Abbreviation Feature1,2-Dioleoyl-sn-glycero-3-phosphatidylcholine DOPC Helper1,2-Dioleoyl-sn-glycero-3-phosphatidylethanolamine DOPE HelperCholesterol Helper N-[1-(2,3-Dioleyloxy)propyl]N,N,N-trimethylammoniumDOT_(m)A Cationic chloride 1,2-Dioleoyloxy-3-trimethylammonium-propaneDOTAP Cationic Dioctadecylamidoglycylspermine DOGS CationicN-(3-Aminopropyl)-N,N-dimethyl-2,3-bis(dodecyloxy)-1- GAP- Cationicpropanaminium bromide DLRIE Cetyltrimethylammonium bromide CTAB Cationic6-Lauroxyhexyl ornithinate LHON Cationic1-(2,3-Dioleoyloxypropyl)-2,4,6-trimethylpyridinium 2Oc Cationic2,3-Dioleyloxy-N-[2(sperminecarboxamido-ethyl]-N,N- DOSPA Cationicdimethyl-1-propanaminium trifluoroacetate1,2-Dioleyl-3-trimethylammonium-propane DOPA CationicN-(2-Hydroxyethyl)-N,N-dimethyl-2,3-bis(tetradecyloxy)-1- MDRIE Cationicpropanaminium bromide Dimyristooxypropyl dimethyl hydroxyethyl ammoniumbromide DMRI Cationic3β-[N-(N′,N′-Dimethylaminoethane)-carbamoyl]cholesterol DC-Chol CationicBis-guanidium-tren-cholesterol BGTC Cationic1,3-Diodeoxy-2-(6-carboxy-spermyl)-propylamide DOSPER CationicDimethyloctadecylammonium bromide DDAB CationicDioctadecylamidoglicylspermidin DSL Cationicrac-[(2,3-Dioctadecyloxypropyl)(2-hydroxyethyl)]- CLIP-1 Cationicdimethylammonium chloride rac-[2(2,3-Dihexadecyloxypropyl- CLIP-6Cationic oxymethyloxy)ethyl]trimethylammonium bromideEthyldimyristoylphosphatidylcholine EDMPC Cationic1,2-Distearyloxy-N,N-dimethyl-3-aminopropane DSDMA Cationic1,2-Dimyristoyl-trimethylammonium propane DMTAP CationicO,O′-Dimyristyl-N-lysyl aspartate DMKE Cationic1,2-Distearoyl-sn-glycero-3-ethylphosphocholine DSEPC CationicN-Palmitoyl D-erythro-sphingosyl carbamoyl-spermine CCS CationicN-t-Butyl-N0-tetradecyl-3-tetradecylaminopropionamidine diC14- Cationicamidine Octadecenolyoxy[ethyl-2-heptadecenyl-3 hydroxyethyl] DOTIMCationic imidazolinium chlorideN1-Cholesteryloxycarbonyl-3,7-diazanonane-1,9-diamine CDAN Cationic2-(3-[Bis(3-amino-propyl)-amino]propylamino)-N- RPR209120 Cationicditetradecylcarbamoylme-ethyl-acetamide1,2-dilinoleyloxy-3-dimethylaminopropane DLinDMA Cationic2,2-dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane DLin-KC2- CationicDMA dilinoleyl-methyl-4-dimethylaminobutyrate DLin-MC3- Cationic DMA

TABLE 2 Cas systems Structure of Families (and encoded superfamily) ofGene System type Name from protein (PDB encoded name^(‡) or subtype Haft2005^(§) accessions)^(¶) protein^(#)** Representatives cas1 Type I cas13GOD, 3LFX COG1518 SERP2463, SPy1047 Type II and 2YZS and ygbT Type IIIcas2 Type I cas2 2IVY, 2I8E and COG1343 and SERP2462, SPy1048, Type II3EXC COG3512 SPy1723 (N-terminal Type III domain) and ygbF cas3′ TypeI^(‡‡) cas3 NA COG1203 APE1232 and ygcB cas3″ Subtype I-A NA NA COG2254APE1231 and Subtype I-B BH0336 cas4 Subtype I-A cas4 and csa1 NA COG1468APE1239 and Subtype I-B BH0340 Subtype I-C Subtype I-D Subtype II-B cas5Subtype I-A cas5a, cas5d, 3KG4 COG1688 APE1234, BH0337, Subtype I-Bcas5e, cas5h, (RAMP) devS and ygcI Subtype I-C cas5p, cas5t Subtype I-Eand cmx5 cas6 Subtype I-A cas6 and cmx6 3I4H COG1583 and PF1131 andslr7014 Subtype I-B COG5551 Subtype I-D (RAMP) Subtype III-A SubtypeIII-B cas6e Subtype I-E cse3 1WJ9 (RAMP) ygcH cas6f Subtype I-F csy42XLJ (RAMP) y1727 cas7 Subtype I-A csa2, csd2, NA COG1857 and devR andygcJ Subtype I-B cse4, csh2, COG3649 Subtype I-C csp1 and cst2 (RAMP)Subtype I-E cas8a1 Subtype I-A^(‡‡) cmx1, cst1, NA BH0338-likeLA3191^(§§) and csx8, csx13 PG2018^(§§) and CXXC- CXXC cas8a2 SubtypeI-A^(‡‡) csa4 and csx9 NA PH0918 AF0070, AF1873, MJ0385, PF0637, PH0918and SSO1401 cas8b Subtype I-B^(‡‡) csh1 and NA BH0338-like MTH1090 andT_(m)1802 T_(m)1802 cas8c Subtype I-C^(‡‡) csd1 and csp2 NA BH0338-likeBH0338 cas9 Type II^(‡‡) csn1 and csx12 NA COG3513 FTN_0757 and SPy1046cas10 Type III^(‡‡) cmr2, csm1 NA COG1353 MTH326, Rv2823c^(§§) and csx11and T_(m)1794^(§§) cas10d Subtype I-D^(‡‡) csc3 NA COG1353 slr7011 csy1Subtype I-F^(‡‡) csy1 NA y1724-like y1724 csy2 Subtype I-F csy2 NA(RAMP) y1725 csy3 Subtype I-F csy3 NA (RAMP) y1726 cse1 Subtype I-E^(‡‡)cse1 NA YgcL-like ygcL cse2 Subtype I-E cse2 2ZCA YgcK-like ygcK csc1Subtype I-D csc1 NA alr1563-like alr1563 (RAMP) csc2 Subtype I-D csc1and csc2 NA COG1337 slr7012 (RAMP) csa5 Subtype I-A csa5 NA AF1870AF1870, MJ0380, PF0643 and SSO1398 csn2 Subtype II-A csn2 NASPy1049-like SPy1049 csm2 Subtype III-A^(‡‡) csm2 NA COG1421 MTH1081 andSERP2460 csm3 Subtype III-A csc2 and csm3 NA COG1337 MTH1080 and (RAMP)SERP2459 csm4 Subtype III-A csm4 NA COG1567 MTH1079 and (RAMP) SERP2458csm5 Subtype III-A csm5 NA COG1332 MTH1078 and (RAMP) SERP2457 csm6Subtype III-A APE2256 and 2WTE COG1517 APE2256 and csm6 SSO1445 cmr1Subtype III-B cmr1 NA COG1367 PF1130 (RAMP) cmr3 Subtype III-B cmr3 NACOG1769 PF1128 (RAMP) cmr4 Subtype III-B cmr4 NA COG1336 PF1126 (RAMP)cmr5 Subtype III-B^(‡‡) cmr5 2ZOP and COG3337 MTH324 and 2OEB PF1125cmr6 Subtype III-B cmr6 NA COG1604 PF1124 (RAMP) csb1 Subtype I-UGSU0053 NA (RAMP) Balac_1306 and GSU0053 csb2 Subtype I-U^(§§) NA NA(RAMP) Balac_1305 and GSU0054 csb3 Subtype I-U NA NA (RAMP)Balac_1303^(§§) csx17 Subtype I-U NA NA NA Btus_2683 csx14 Subtype I-UNA NA NA GSU0052 csx10 Subtype I-U csx10 NA (RAMP) Caur_2274 csx16Subtype III-U VVA1548 NA NA WA1548 csaX Subtype III-U csaX NA NA SSO1438csx3 Subtype III-U csx3 NA NA AF1864 csx1 Subtype III-U csa3, csx1, 1XMXand COG1517 and MJ1666, NE0113, csx2, DXTHG, 2I71 COG4006 PF1127 andNE0113 and T_(m)1812 TIGR02710 csx15 Unknown NA NA TTE2665 TTE2665 csf1Type U csf1 NA NA AFE_1038 csf2 Type U csf2 NA (RAMP) AFE_1039 csf3 TypeU csf3 NA (RAMP) AFE_1040 csf4 Type U csf4 NA NA AFE_1037

TABLE 3 Component formulation, delivery, and administration strategiesElements Donor Template Cas9 gRNA Nucleic Molecule(s) Molecule(s) AcidComments DNA DNA DNA In this embodiment, a Cas9 molecule, typically aneaCas9 molecule, and a gRNA are transcribed from DNA. In thisembodiment, they are encoded on separate molecules. In this embodiment,the donor template is provided as a separate DNA molecule. DNA DNA Inthis embodiment, a Cas9 molecule, typically an eaCas9 molecule, and agRNA are transcribed from DNA. In this embodiment, they are encoded onseparate molecules. In this embodiment, the donor template is providedon the same DNA molecule that encodes the gRNA. DNA DNA In thisembodiment, a Cas9 molecule, typically an eaCas9 molecule, and a gRNAare transcribed from DNA, here from a single molecule. In thisembodiment, the donor template is provided as a separate DNA molecule.DNA DNA DNA In this embodiment, a Cas9 molecule, typically an eaCas9molecule, and a gRNA are transcribed from DNA. In this embodiment, theyare encoded on separate molecules. In this embodiment, the donortemplate is provided on the same DNA molecule that encodes the Cas9. DNARNA DNA In this embodiment, a Cas9 molecule, typically an eaCas9molecule, is transcribed from DNA, and a gRNA is provided as in vitrotranscribed or synthesized RNA. In this embodiment, the donor templateis provided as a separate DNA molecule. DNA RNA DNA In this embodiment,a Cas9 molecule, typically an eaCas9 molecule, is transcribed from DNA,and a gRNA is provided as in vitro transcribed or synthesized RNA. Inthis embodiment, the donor template is provided on the same DNA moleculethat encodes the Cas9. mRNA RNA DNA In this embodiment, a Cas9 molecule,typically an eaCas9 molecule, is translated from in vitro transcribedmRNA, and a gRNA is provided as in vitro transcribed or synthesized RNA.In this embodiment, the donor template is provided as a DNA molecule.mRNA DNA DNA In this embodiment, a Cas9 molecule, typically an eaCas9molecule, is translated from in vitro transcribed mRNA, and a gRNA istranscribed from DNA. In this embodiment, the donor template is providedas a separate DNA molecule. mRNA DNA In this embodiment, a Cas9molecule, typically an eaCas9 molecule, is translated from in vitrotranscribed mRNA, and a gRNA is transcribed from DNA. In thisembodiment, the donor template is provided on the same DNA molecule thatencodes the gRNA. Protein DNA DNA In this embodiment, a Cas9 molecule,typically an eaCas9 molecule, is provided as a protein, and a gRNA istranscribed from DNA. In this embodiment, the donor template is providedas a separate DNA molecule. Protein DNA In this embodiment, a Cas9molecule, typically an eaCas9 molecule, is provided as a protein, and agRNA is transcribed from DNA. In this embodiment, the donor template isprovided on the same DNA molecule that encodes the gRNA. Protein RNA DNAIn this embodiment, an eaCas9 molecule is provided as a protein, and agRNA is provided as transcribed or synthesized RNA. In this embodiment,the donor template is provided as a DNA molecule.

TABLE 4 Delivery methods for Cas system components Delivery Vector/ModeDelivery into Duration Type of Non-Dividing of Genome Molecule CellsExpression Integration Delivered Physical (e.g., YES Transient NONucleic Acids electroporation, particle gun, and Proteins CalciumPhosphate transfection, cell compression or squeezing) Viral RetrovirusNO Stable YES RNA Lentivirus YES Stable YES/NO with RNA modificationsAdenovirus YES Transient NO DNA Adeno- YES Stable NO DNA AssociatedVirus (AAV) Vaccinia Virus YES Very NO DNA Transient Herpes Simplex YESStable NO DNA Virus Non-Viral Cationic YES Transient Depends on NucleicAcids Liposomes what is and Proteins delivered Polymeric YES TransientDepends on Nucleic Acids Nanoparticles what is and Proteins deliveredBiological Attenuated YES Transient NO Nucleic Acids Non-Viral BacteriaDelivery Engineered YES Transient NO Nucleic Acids VehiclesBacteriophages Mammalian YES Transient NO Nucleic Acids Virus-likeParticles Biological YES Transient NO Nucleic Acids liposomes:Erythrocyte Ghosts and Exosomes

TABLE 5 Polymers used for gene transfer Polymer AbbreviationPoly(ethylene)glycol PEG Polyethylenimine PEIDithiobis(succinimidylpropionate) DSPDimethyl-3,3′-dithiobispropionimidate DTBP Poly(ethylene imine)biscarbamate PEIC Poly(L-lysine) PLL Histidine modified PLLPoly(N-vinylpyrrolidone) PVP Poly(propylenimine) PPI Poly(amidoamine)PAMAM Poly(amido ethylenimine) SS-PAEI Triethylenetetramine TETAPoly(β-aminoester) Poly(4-hydroxy-L-proline ester) PHP Poly(allylamine)Poly(α-[4-aminobutyl]-L-glycolic acid) PAGA Poly(D,L-lactic-co-glycolicacid) PLGA Poly(N-ethyl-4-vinylpyridinium bromide) Poly(phosphazene)sPPZ Poly(phosphoester)s PPE Poly(phosphoramidate)s PPAPoly(N-2-hydroxypropylmethacrylamide) pHPMA Poly (2-(dimethylamino)ethylmethacrylate) pDMAEMA Poly(2-aminoethyl propylene phosphate) PPE-EAChitosan Galactosylated chitosan N-Dodacylated chitosan Histone CollagenDextran-spermine D-SPM

TABLE 6 Synthesis or manufacturer Sequence of T_(m) Delta % routegRNA molecule ° C. T_(m) NHEJ Purchased GUAACGGCAGACUUC 50 8 26.14 fromUCCUCGUUUUAGAGC Company 1 UAGAAAUAGCAAGUU AAAAUAAGGCUAGUCCGUUAUCAACUUGAA AAAGUGGCACCGAGU CGGUGCUUUU (SEQ ID NO: 208) SynthesizedGUAACGGCAGACUUC 44 2 11.64 from UCCUCGUUUUAGAGC Company 2UAGAAAUAGCAAGUU AAAAUAAGGCUAGUC CGUUAUCAACUUGAA AAAGUGGCACCGAGUCGGUGCUUUU (SEQ ID NO: 208) In vitro GUAACGGCAGACUUC 50 8 27.33transcribed UCCUCGUUUUAGAGC using UAGAAAUAGCAAGUU MEGAshortscript™AAAAUAAGGCUAGUC T7 Kit CGUUAUCAACUUGAA AAAGUGGCACCGAGU CGGUGCUUUU(SEQ ID NO: 208) Synthesized GGUAACGGCAGACUU 47 5 11.43 fromCUCCUCGUUUUAGAG Company 2 CUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGA AAAAGUGGCACCGAG UCGGUGCUUUU (SEQ ID NO: 209) In vitroGGGUAACGGCAGACU 51 9 22.74 transcribed UCUCCUCGUUUUAGA usingGCUAGAAAUAGCAAG MEGAshortscript™ UUAAAAUAAGGCUAG T7 Kit UCCGUUAUCAACUUGAAAAAGUGGCACCGA GUCGGUGCUUUU (SEQ ID NO: 210)

1-57. (canceled)
 58. A method of screening for a Cas9 molecule/gRNAmolecule complex, the method comprising: (a) generating a plurality ofsamples, each sample comprising a Cas9 molecule/gRNA molecule complexgenerated by combining a Cas9 molecule and one of a plurality of gRNAmolecules; (b) detecting a melting temperature (T_(m)) value of the Cas9molecule/gRNA molecule complex in each of the plurality of samples; and(c) selecting at least one sample from the plurality of samples based ona comparison of the T_(m) values in the plurality of samples to a T_(m)value of a reference molecule or a T_(m) reference value.
 59. The methodof claim 58, wherein the T_(m) value is detected using a thermal shiftassay.
 60. The method of claim 59, wherein the thermal shift assay isselected from differential scanning fluorimetry (DSF), differentialscanning calorimetry (DSC), or isothermal titration calorimetry (ITC).61. The method of claim 60, wherein the sample is selected if the T_(m)value of the Cas9 molecule/gRNA molecule complex in the sample is atleast 1° C., at least 2° C., at least 3° C., at least 4° C., at least 5°C., at least 6° C., at least 7° C., at least 8° C., at least 9° C., atleast 10° C., at least 11° C., at least 12° C., at least 13° C., atleast 14° C., at least 15° C., at least 16° C., at least 17° C., atleast 18° C., at least 19° C., or at least 20° C. greater than the T_(m)value of the reference molecule or the T_(m) reference value.
 62. Themethod of claim 61, wherein the reference molecule is selected from thegroup consisting of: (a) a reference Cas9 molecule in the absence of agRNA molecule; (b) a reference Cas9 molecule complexed with a gRNAmolecule different from the first gRNA molecule in the complex beingevaluated; and (c) a reference Cas9 molecule/gRNA molecule complexformed under a different condition or buffer than the Cas9 molecule/gRNAmolecule complex being evaluated.
 63. The method of claim 62, whereinthe condition comprises using a proportion of Cas9 molecule and gRNAmolecule relative to the complex being evaluated.
 64. A method ofdetermining the stability of a Cas9 molecule/gRNA molecule complex, themethod comprising: (a) generating a plurality of Cas9 molecule/gRNAmolecule complexes, each comprising a Cas9 molecule/gRNA moleculecomplex generated by combining a Cas9 molecule and one of a plurality ofgRNA molecules; (b) detecting a melting temperature (T_(m)) value ofeach of the Cas9 molecule/gRNA molecule complexes of the plurality ofCas9 molecule/gRNA molecule complexes; and (c) determining one or moreof the plurality of Cas9 molecule/gRNA molecule complexes is stable ifthe T_(m) value of the Cas9 molecule/gRNA molecule complex is greaterthan a T_(m) value of a reference molecule or a T_(m) reference value.65. The method of claim 64, wherein the T_(m) value is detected using athermal shift assay.
 66. The method of claim 65, wherein the thermalshift assay is selected from differential scanning fluorimetry (DSF),differential scanning calorimetry (DSC), or isothermal titrationcalorimetry (ITC).
 67. The method of claim 66, wherein the Cas9molecule/gRNA molecule complex is stable if the T_(m) value of the Cas9molecule/gRNA molecule complex in the sample is at least 1° C., at least2° C., at least 3° C., at least 4° C., at least 5° C., at least 6° C.,at least 7° C., at least 8° C., at least 9° C., at least 10° C., atleast 11° C., at least 12° C., at least 13° C., at least 14° C., atleast 15° C., at least 16° C., at least 17° C., at least 18° C., atleast 19° C., or at least 20° C. greater than the T_(m) value of thereference molecule or the T_(m) reference value.
 68. The method of claim67, wherein the reference molecule is selected from the group consistingof: (a) a reference Cas9 molecule in the absence of a gRNA molecule; (b)a reference Cas9 molecule complexed with a gRNA molecule different fromthe first gRNA molecule in the complex being evaluated; and (c) areference Cas9 molecule/gRNA molecule complex formed under a differentcondition or buffer than the Cas9 molecule/gRNA molecule complex beingevaluated.
 69. The method of claim 68, wherein the condition comprisesusing a proportion of Cas9 molecule and gRNA molecule relative to thecomplex being evaluated.
 70. A method of determining the stability of aCas9 molecule/gRNA molecule complex, the method comprising: (a)combining a Cas9 molecule and a gRNA molecule in a sample to form theCas9 molecule/gRNA molecule complex; (b) detecting a melting temperature(T_(m)) value of the Cas9 molecule/gRNA molecule complex; (c) measuringan activity value of the Cas9 molecule/gRNA molecule complex; and (d)determining the Cas9 molecule/gRNA molecule complex is stable if (i) theT_(m) value of the Cas9 molecule/gRNA molecule complex is greater than aT_(m) value of a reference molecule or a T_(m) reference value and (ii)the activity value of the Cas9 molecule/gRNA molecule complex is greaterthan an activity value of a reference molecule or an activity referencevalue.
 71. The method of claim 70, wherein the activity comprises one ormore of: an ability to induce indels; an ability to modify a target DNA;a propensity of a preselected repair method; an ability of the gRNAmolecule to remain hybridized to the DNA target; and an ability of thegRNA molecule to bind to the Cas9 molecule of the Cas9 molecule/gRNAmolecule complex.
 72. The method of claim 71, wherein the activity valueis a binding value and the activity is the ability of the gRNA moleculeto bind to the Cas9 molecule comprising: combining the gRNA molecule andthe Cas9 molecule in a sample to form the Cas9 molecule/gRNA moleculecomplex; measuring a binding value of the Cas9 molecule/gRNA moleculecomplex; and determining the Cas9 molecule/gRNA molecule complex isstable if the binding value of the Cas9 molecule/gRNA molecule complexis greater than the binding value of a reference molecule or the bindingreference value
 73. The method of claim 72, wherein the binding value ismeasured using a kinetics assay.
 74. The method of claim 73, wherein thekinetics assay is selected from surface plasmon resonance (SPR) assay,Bio-Layer Interferometry (BLI) assay, or gel band shift assay.
 75. Themethod of claim 74, wherein the T_(m) value is detected using a thermalshift assay.
 76. The method of claim 75, wherein the thermal shift assayis selected from differential scanning fluorimetry (DSF), differentialscanning calorimetry (DSC), or isothermal titration calorimetry (ITC).77. The method of claim 76, wherein the Cas9 molecule/gRNA moleculecomplex is stable if the T_(m) value of the Cas9 molecule/gRNA moleculecomplex in the sample is at least 1° C., at least 2° C., at least 3° C.,at least 4° C., at least 5° C., at least 6° C., at least 7° C., at least8° C., at least 9° C., at least 10° C., at least 11° C., at least 12°C., at least 13° C., at least 14° C., at least 15° C., at least 16° C.,at least 17° C., at least 18° C., at least 19° C., or at least 20° C.greater than the T_(m) value of the reference molecule or the T_(m)reference value.